diff --git a/.github/workflows/bumpversion.yml b/.github/workflows/bumpversion.yml
new file mode 100644
index 00000000..e54a5898
--- /dev/null
+++ b/.github/workflows/bumpversion.yml
@@ -0,0 +1,66 @@
+name: Bump version
+
+on:
+  push:
+    branches:
+      - master
+
+jobs:
+  bump-version:
+    if: "!startsWith(github.event.head_commit.message, 'bump:')"
+    runs-on: ubuntu-latest
+    name: "Bump version and create changelog with commitizen"
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+
+      - name: Run image
+        uses: abatilo/actions-poetry@v2.0.0
+        with:
+          poetry-version: 1.1.8
+      - name: Cache Poetry virtualenv
+        uses: actions/cache@v1
+        id: cache
+        with:
+          path: ~/.virtualenvs
+          key: venv-${{ matrix.os }}-${{ matrix.python-version }}-${{ hashFiles('**/poetry.lock') }}
+          restore-keys: |
+            venv-${{ matrix.os }}-${{ matrix.python-version }}-
+
+      - name: Set Poetry config
+        run: |
+          poetry config virtualenvs.in-project false
+          poetry config virtualenvs.path ~/.virtualenvs
+
+      - name: Install Dependencies
+        run: poetry install
+        if: steps.cache.outputs.cache-hit != 'true'
+      
+      - name: Verify github tags
+        run: |
+          git config --global user.name '${{ github.actor }}'
+          git config --global user.email '${{ github.actor }}@users.noreply.github.com'
+          git remote set-url origin https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/$GITHUB_REPOSITORY
+          git checkout $GITHUB_HEAD_REF
+          git fetch --all --tags
+          git tag
+
+      # - name: Create bump and changelog
+      #   uses: commitizen-tools/commitizen-action@master
+      #   with:
+      #     github_token: ${{ secrets.GITHUB_TOKEN }}
+      
+      - name: Create bump and changelog
+        run: |
+          poetry run cz bump --changelog
+
+      - name: Push changelog, version files and new tag
+        run: |
+          git config --global user.name '${{ github.actor }}'
+          git config --global user.email '${{ github.actor }}@users.noreply.github.com'
+          git remote set-url origin https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/$GITHUB_REPOSITORY
+          git checkout $GITHUB_HEAD_REF
+          git push --force
+          git push --tags --force
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
new file mode 100644
index 00000000..7414a094
--- /dev/null
+++ b/.github/workflows/ci.yml
@@ -0,0 +1,65 @@
+name: ci
+
+on: [push]
+
+jobs:
+
+  CI:
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.7]
+        os: [ubuntu-18.04, macos-latest, windows-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Run image
+        uses: abatilo/actions-poetry@v2.0.0
+        with:
+          poetry-version: 1.1.8
+      - name: Cache Poetry virtualenv
+        uses: actions/cache@v1
+        id: cache
+        with:
+          path: ~/.virtualenvs
+          key: venv-${{ matrix.os }}-${{ matrix.python-version }}-${{ hashFiles('**/poetry.lock') }}
+          restore-keys: |
+            venv-${{ matrix.os }}-${{ matrix.python-version }}-
+
+      - name: Set Poetry config
+        run: |
+          poetry config virtualenvs.in-project false
+          poetry config virtualenvs.path ~/.virtualenvs
+
+      - name: Install Dependencies
+        run: poetry install
+        if: steps.cache.outputs.cache-hit != 'true'
+
+      - name: Test with pytest
+        run: poetry run pytest --cov . --cov-report xml:coverage-reports/coverage-fm2prof-src.xml --junitxml=xunit-reports/xunit-result-fm2prof-src.xml
+
+      - name: Autoformat code if the check fails
+        if: ${{ (matrix.os == 'ubuntu-18.04') && (matrix.python-version == 3.8) }}
+        run: |
+          poetry run isort .
+          poetry run black .
+          git config --global user.name '${{ github.actor }}'
+          git config --global user.email '${{ github.actor }}@users.noreply.github.com'
+          git remote set-url origin https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/$GITHUB_REPOSITORY
+          git checkout $GITHUB_HEAD_REF
+          git commit -am "autoformat: isort & black" && git push || true
+
+      - name: SonarCloud Scan
+        uses: SonarSource/sonarcloud-github-action@master
+        if: ${{ (matrix.os == 'ubuntu-18.04') && (matrix.python-version == 3.8) }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
\ No newline at end of file
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
new file mode 100644
index 00000000..5a0f48a6
--- /dev/null
+++ b/.github/workflows/docs.yml
@@ -0,0 +1,40 @@
+name: docs
+on:
+  push:
+    branches:
+      - master
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+
+      - name: Run image
+        uses: abatilo/actions-poetry@v2.0.0
+        with:
+          poetry-version: 1.1.8
+      - name: Cache Poetry virtualenv
+        uses: actions/cache@v1
+        id: cache
+        with:
+          path: ~/.virtualenvs
+          key: venv-${{ matrix.os }}-${{ matrix.python-version }}-${{ hashFiles('**/poetry.lock') }}
+          restore-keys: |
+            venv-${{ matrix.os }}-${{ matrix.python-version }}-
+
+      - name: Set Poetry config
+        run: |
+          poetry config virtualenvs.in-project false
+          poetry config virtualenvs.path ~/.virtualenvs
+
+      - name: Install Dependencies
+        run: poetry install
+        if: steps.cache.outputs.cache-hit != 'true'
+      
+      - name: Build SPHINX docs
+        uses: ammaraskar/sphinx-action@master
+        with:
+          docs-folder: "docs/"
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 00000000..8cba7953
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,3 @@
+.vscode
+.pytest_cache
+**__pycache__**
\ No newline at end of file
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 00000000..f0dc5342
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,6 @@
+repos:
+  - repo: https://github.com/commitizen-tools/commitizen
+    rev: v2.20.0
+    hooks:
+      - id: commitizen
+        stages: [commit-msg]
\ No newline at end of file
diff --git a/CHANGELOG.rst b/docs/CHANGELOG.rst
similarity index 100%
rename from CHANGELOG.rst
rename to docs/CHANGELOG.rst
diff --git a/environment.yml b/environment.yml
index 1dbdf3c9..fcde2068 100644
--- a/environment.yml
+++ b/environment.yml
@@ -2,7 +2,7 @@ name: fm2prof
 channels:
   - defaults
 dependencies:
-  - python=3.6
+  - python=3.7
   - netCDF4
   - scipy
   - numpy
@@ -10,7 +10,6 @@ dependencies:
   - matplotlib
   - shapely
   - pylint
-  - netcdf4
   - scikit-learn
   - pytest
   - jupyter
diff --git a/fm2prof/__init__.py b/fm2prof/__init__.py
index f8f75418..527de7d4 100644
--- a/fm2prof/__init__.py
+++ b/fm2prof/__init__.py
@@ -1,2 +1,4 @@
+__version__ = "1.4.3"
+
 from fm2prof.Fm2ProfRunner import Project
-from fm2prof import utils
\ No newline at end of file
+from fm2prof import utils
diff --git a/poetry.lock b/poetry.lock
new file mode 100644
index 00000000..2409ddb0
--- /dev/null
+++ b/poetry.lock
@@ -0,0 +1,1760 @@
+[[package]]
+name = "alabaster"
+version = "0.7.12"
+description = "A configurable sidebar-enabled Sphinx theme"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "argcomplete"
+version = "1.12.3"
+description = "Bash tab completion for argparse"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+importlib-metadata = {version = ">=0.23,<5", markers = "python_version == \"3.7\""}
+
+[package.extras]
+test = ["coverage", "flake8", "pexpect", "wheel"]
+
+[[package]]
+name = "atomicwrites"
+version = "1.4.0"
+description = "Atomic file writes."
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+
+[[package]]
+name = "attrs"
+version = "21.2.0"
+description = "Classes Without Boilerplate"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+
+[package.extras]
+dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit"]
+docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
+tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface"]
+tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins"]
+
+[[package]]
+name = "babel"
+version = "2.9.1"
+description = "Internationalization utilities"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+
+[package.dependencies]
+pytz = ">=2015.7"
+
+[[package]]
+name = "backports.entry-points-selectable"
+version = "1.1.1"
+description = "Compatibility shim providing selectable entry points for older implementations"
+category = "dev"
+optional = false
+python-versions = ">=2.7"
+
+[package.dependencies]
+importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
+
+[package.extras]
+docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
+testing = ["pytest", "pytest-flake8", "pytest-cov", "pytest-black (>=0.3.7)", "pytest-mypy", "pytest-checkdocs (>=2.4)", "pytest-enabler (>=1.0.1)"]
+
+[[package]]
+name = "black"
+version = "21.11b1"
+description = "The uncompromising code formatter."
+category = "dev"
+optional = false
+python-versions = ">=3.6.2"
+
+[package.dependencies]
+click = ">=7.1.2"
+mypy-extensions = ">=0.4.3"
+pathspec = ">=0.9.0,<1"
+platformdirs = ">=2"
+regex = ">=2021.4.4"
+tomli = ">=0.2.6,<2.0.0"
+typed-ast = {version = ">=1.4.2", markers = "python_version < \"3.8\" and implementation_name == \"cpython\""}
+typing-extensions = [
+    {version = ">=3.10.0.0", markers = "python_version < \"3.10\""},
+    {version = "!=3.10.0.1", markers = "python_version >= \"3.10\""},
+]
+
+[package.extras]
+colorama = ["colorama (>=0.4.3)"]
+d = ["aiohttp (>=3.7.4)"]
+jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
+python2 = ["typed-ast (>=1.4.3)"]
+uvloop = ["uvloop (>=0.15.2)"]
+
+[[package]]
+name = "certifi"
+version = "2021.10.8"
+description = "Python package for providing Mozilla's CA Bundle."
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "cfgv"
+version = "3.3.1"
+description = "Validate configuration and produce human readable error messages."
+category = "dev"
+optional = false
+python-versions = ">=3.6.1"
+
+[[package]]
+name = "cftime"
+version = "1.5.1.1"
+description = "Time-handling functionality from netcdf4-python"
+category = "main"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+numpy = "*"
+
+[[package]]
+name = "charset-normalizer"
+version = "2.0.8"
+description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
+category = "dev"
+optional = false
+python-versions = ">=3.5.0"
+
+[package.extras]
+unicode_backport = ["unicodedata2"]
+
+[[package]]
+name = "click"
+version = "8.0.3"
+description = "Composable command line interface toolkit"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+colorama = {version = "*", markers = "platform_system == \"Windows\""}
+importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
+
+[[package]]
+name = "colorama"
+version = "0.4.4"
+description = "Cross-platform colored terminal text."
+category = "main"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+
+[[package]]
+name = "commitizen"
+version = "2.20.0"
+description = "Python commitizen client tool"
+category = "dev"
+optional = false
+python-versions = ">=3.6.1,<4.0.0"
+
+[package.dependencies]
+argcomplete = ">=1.12.1,<2.0.0"
+colorama = ">=0.4.1,<0.5.0"
+decli = ">=0.5.2,<0.6.0"
+jinja2 = ">=2.10.3"
+packaging = ">=19,<22"
+pyyaml = ">=3.08"
+questionary = ">=1.4.0,<2.0.0"
+termcolor = ">=1.1,<2.0"
+tomlkit = ">=0.5.3,<1.0.0"
+
+[[package]]
+name = "coverage"
+version = "6.2"
+description = "Code coverage measurement for Python"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+tomli = {version = "*", optional = true, markers = "extra == \"toml\""}
+
+[package.extras]
+toml = ["tomli"]
+
+[[package]]
+name = "cycler"
+version = "0.11.0"
+description = "Composable style cycles"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[[package]]
+name = "decli"
+version = "0.5.2"
+description = "Minimal, easy-to-use, declarative cli tool"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[[package]]
+name = "distlib"
+version = "0.3.3"
+description = "Distribution utilities"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "docutils"
+version = "0.17.1"
+description = "Docutils -- Python Documentation Utilities"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+
+[[package]]
+name = "filelock"
+version = "3.4.0"
+description = "A platform independent file lock."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.extras]
+docs = ["furo (>=2021.8.17b43)", "sphinx (>=4.1)", "sphinx-autodoc-typehints (>=1.12)"]
+testing = ["covdefaults (>=1.2.0)", "coverage (>=4)", "pytest (>=4)", "pytest-cov", "pytest-timeout (>=1.4.2)"]
+
+[[package]]
+name = "fonttools"
+version = "4.28.2"
+description = "Tools to manipulate font files"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
+[package.extras]
+all = ["fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "zopfli (>=0.1.4)", "lz4 (>=1.7.4.2)", "matplotlib", "sympy", "skia-pathops (>=0.5.0)", "brotlicffi (>=0.8.0)", "scipy", "brotli (>=1.0.1)", "munkres", "unicodedata2 (>=13.0.0)", "xattr"]
+graphite = ["lz4 (>=1.7.4.2)"]
+interpolatable = ["scipy", "munkres"]
+lxml = ["lxml (>=4.0,<5)"]
+pathops = ["skia-pathops (>=0.5.0)"]
+plot = ["matplotlib"]
+symfont = ["sympy"]
+type1 = ["xattr"]
+ufo = ["fs (>=2.2.0,<3)"]
+unicode = ["unicodedata2 (>=13.0.0)"]
+woff = ["zopfli (>=0.1.4)", "brotlicffi (>=0.8.0)", "brotli (>=1.0.1)"]
+
+[[package]]
+name = "geojson"
+version = "2.5.0"
+description = "Python bindings and utilities for GeoJSON"
+category = "main"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "identify"
+version = "2.4.0"
+description = "File identification library for Python"
+category = "dev"
+optional = false
+python-versions = ">=3.6.1"
+
+[package.extras]
+license = ["ukkonen"]
+
+[[package]]
+name = "idna"
+version = "3.3"
+description = "Internationalized Domain Names in Applications (IDNA)"
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
+[[package]]
+name = "imagesize"
+version = "1.3.0"
+description = "Getting image size from png/jpeg/jpeg2000/gif file"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+
+[[package]]
+name = "importlib-metadata"
+version = "4.8.2"
+description = "Read metadata from Python packages"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""}
+zipp = ">=0.5"
+
+[package.extras]
+docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
+perf = ["ipython"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
+
+[[package]]
+name = "iniconfig"
+version = "1.1.1"
+description = "iniconfig: brain-dead simple config-ini parsing"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "isort"
+version = "5.10.1"
+description = "A Python utility / library to sort Python imports."
+category = "dev"
+optional = false
+python-versions = ">=3.6.1,<4.0"
+
+[package.extras]
+pipfile_deprecated_finder = ["pipreqs", "requirementslib"]
+requirements_deprecated_finder = ["pipreqs", "pip-api"]
+colors = ["colorama (>=0.4.3,<0.5.0)"]
+plugins = ["setuptools"]
+
+[[package]]
+name = "jinja2"
+version = "3.0.3"
+description = "A very fast and expressive template engine."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+MarkupSafe = ">=2.0"
+
+[package.extras]
+i18n = ["Babel (>=2.7)"]
+
+[[package]]
+name = "kiwisolver"
+version = "1.3.2"
+description = "A fast implementation of the Cassowary constraint solver"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
+[[package]]
+name = "markupsafe"
+version = "2.0.1"
+description = "Safely add untrusted strings to HTML/XML markup."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[[package]]
+name = "matplotlib"
+version = "3.5.0"
+description = "Python plotting package"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+cycler = ">=0.10"
+fonttools = ">=4.22.0"
+kiwisolver = ">=1.0.1"
+numpy = ">=1.17"
+packaging = ">=20.0"
+pillow = ">=6.2.0"
+pyparsing = ">=2.2.1"
+python-dateutil = ">=2.7"
+setuptools_scm = ">=4"
+
+[[package]]
+name = "mypy-extensions"
+version = "0.4.3"
+description = "Experimental type system extensions for programs checked with the mypy typechecker."
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "netcdf4"
+version = "1.5.0"
+description = "Provides an object-oriented python interface to the netCDF version 4 library."
+category = "main"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+cftime = "*"
+numpy = ">=1.7"
+
+[[package]]
+name = "nodeenv"
+version = "1.6.0"
+description = "Node.js virtual environment builder"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "numpy"
+version = "1.21.1"
+description = "NumPy is the fundamental package for array computing with Python."
+category = "main"
+optional = false
+python-versions = ">=3.7"
+
+[[package]]
+name = "packaging"
+version = "21.3"
+description = "Core utilities for Python packages"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"
+
+[[package]]
+name = "pandas"
+version = "1.3.4"
+description = "Powerful data structures for data analysis, time series, and statistics"
+category = "main"
+optional = false
+python-versions = ">=3.7.1"
+
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+]
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+    {file = "zipp-3.6.0-py3-none-any.whl", hash = "sha256:9fe5ea21568a0a70e50f273397638d39b03353731e6cbbb3fd8502a33fec40bc"},
+    {file = "zipp-3.6.0.tar.gz", hash = "sha256:71c644c5369f4a6e07636f0aa966270449561fcea2e3d6747b8d23efaa9d7832"},
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diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 00000000..3b67ab32
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,89 @@
+[tool.poetry]
+name = "fm2prof"
+version = "1.4.3"
+description = "Package use to reduce Delft3D FM models from 2D models to 1D models"
+authors = ["K.D. Berends <koen.berends@deltares.nl>"]
+maintainers = ["Carles S. Soriano Perez <carles.sorianoperez@deltares.nl>"]
+license = "GNU LGPL"
+packages = [
+  { include = "fm2prof" },
+]
+
+[tool.poetry.dependencies]
+python = "^3.7"
+seaborn = "^0.7"
+pandas = "^1.3.4"
+numpy = "^1.14"
+netCDF4 = "1.5"
+scipy = "^1.0"
+scikit-learn = "^0.19.0"
+geojson = "^2.4.1"
+Shapely = "^1.8.0"
+click = "^8.0.3"
+matplotlib = "^3.5.0"
+
+[tool.poetry.dev-dependencies]
+pytest = "^6.2.5"
+pytest-cov = "^3.0.0"
+black = "^21.11b1"
+isort = "^5.10.1"
+Sphinx = "^4.3.1"
+commitizen = "^2.20.0"
+pre-commit = "^2.15.0"
+poetry2conda = "^0.3.0"
+
+[tool.commitizen]
+name = "cz_conventional_commits"
+changelog_file = "docs/CHANGELOG.rst"
+update_changelog_on_bump = true
+version = "1.4.3"
+tag_format = "v$major.$minor.$patch"
+version_files = [
+    "fm2prof/__init__.py",
+    "pyproject.toml:version"
+]
+
+[tool.commitizen.custommize]
+bump_pattern = "^(break|new|fix|hotfix|refactor|docs)"
+bump_map = {"break" = "MAJOR", "new" = "MINOR", "fix" = "PATCH", "hotfix" = "PATCH", "refactor"="PATCH", "docs" = "PATCH"}
+
+[tool.coverage.run]
+omit = [
+    "test/*",
+    "docs/*"
+    ]
+
+[tool.black]
+line-length = 88
+target-version = ['py37', 'py38']
+exclude = '''
+(
+  /(
+      \.eggs         # exclude a few common directories in the
+    | \.git          # root of the project
+    | \.hg
+    | \.mypy_cache
+    | \.tox
+    | \.venv
+    | _build
+    | buck-out
+    | build
+    | dist
+    | \.virtualenvs
+  )/
+)
+'''
+
+[tool.isort]
+profile = "black"
+multi_line_output = 3
+line_length = 88
+
+[build-system]
+requires = ["poetry-core>=1.0.4"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.poetry2conda.dependencies]
+pandas = { channel = "conda-forge" }
+netCDF4 = { channel = "conda-forge" }
+shapely = { channel = "conda-forge" }
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 73d54e56..00000000
--- a/setup.py
+++ /dev/null
@@ -1,29 +0,0 @@
-from setuptools import setup, find_packages
-
-# more info: https://docs.python.org/3/distutils/setupscript.html
-# https://docs.pytest.org/en/latest/goodpractices.html#choosing-a-test-layout-import-rules
-
-setup(
-    name="fm2prof",
-    packages=(find_packages(exclude=('tests', 'ReportGenerator'))),
-    # package_dir={'fm2prof': 'fm2prof'},
-    version='1.4.0',
-    description='Package use to reduce Delft3D FM models from 2D models to 1D models',
-    license='LICENSE.txt',
-    long_description=open('README.txt').read(),
-    author='K.D. Berends',
-    author_email='koen.berends@deltares.nl',
-    url='https://www.deltares.nl/nl/',
-    download_url='https://repos.deltares.nl/repos/RIVmodels/rivtools/branches/fm2profTool',
-    install_requires=[
-        "seaborn>=0.7",
-        "pandas>=0.18",
-        "numpy>=1.12",
-        "matplotlib>=1.5",
-        "netCDF4>=1.2.9",
-        "scipy>=1.0",
-        "scikit_learn>=0.19.0",
-        "geojson>=2.4.1",
-        "shapely"
-    ],
-)
diff --git a/tests/TestUtils.py b/tests/TestUtils.py
index 8d436602..d719331c 100644
--- a/tests/TestUtils.py
+++ b/tests/TestUtils.py
@@ -1,15 +1,24 @@
-import sys
+import contextlib
 import os
+import shutil
+import sys
+from pathlib import Path
+from typing import List
+
+import pytest
+
 try:
     from pip import main as pipmain
-except:
+except Exception as e_info:
     from pip._internal import main as pipmain
 
 
 class TestUtils:
 
-    _name_external = 'external_test_data'
-    _name_local = 'test_data'
+    _name_external = "external_test_data"
+    _name_local = "test_data"
+    _name_artifacts = "artifacts"
+    _temp_copies = "temp-copies"
 
     @staticmethod
     def install_package(package: str):
@@ -19,70 +28,59 @@ def install_package(package: str):
         Arguments:
             package {str} -- Name of the PIP package.
         """
-        pipmain(['install', package])
+        pipmain(["install", package])
+
+    @staticmethod
+    def get_external_test_data_dir() -> Path:
+        return Path(__file__).parent / TestUtils._name_external
 
     @staticmethod
-    def get_local_test_data_dir(dir_name: str):
+    def get_local_test_data_dir(dir_name: str) -> Path:
         """
         Returns the desired directory relative to the test data.
         Avoiding extra code on the tests.
         """
-        directory = TestUtils.get_test_data_dir(
-            dir_name, TestUtils._name_local)
+        directory = TestUtils.get_test_data_dir(dir_name, TestUtils._name_local)
         return directory
 
     @staticmethod
-    def get_external_test_data_dir(dir_name: str):
+    def get_external_repo(dir_name: str) -> Path:
         """
-        Returns the desired directory relative to the test external data.
-        Avoiding extra code on the tests.
+        Returns the parent directory of this repo directory.
+
+        Args:
+            dir_name (str): Repo 'sibbling' of the current one.
+
+        Returns:
+            Path: Path to the sibbling repo.
         """
-        directory = TestUtils.get_test_data_dir(
-            dir_name, TestUtils._name_external)
-        return directory
+        return Path(__file__).parent.parent.parent / dir_name
 
     @staticmethod
-    def get_test_data_dir(dir_name: str, test_data_name: str):
+    def get_test_data_dir(dir_name: str, test_data_name: str) -> Path:
         """
         Returns the desired directory relative to the test external data.
         Avoiding extra code on the tests.
         """
-        test_dir = os.path.dirname(__file__)
-        try:
-            dir_path = '{}\\{}\\'.format(test_data_name, dir_name)
-            test_dir = os.path.join(test_dir, dir_path)
-        except Exception:
-            print("An error occurred trying to find {}".format(dir_name))
-        return test_dir
+        return Path(__file__).parent / test_data_name / dir_name
 
     @staticmethod
-    def get_test_dir(dir_name: str):
-        """Returns the desired directory inside the Tests folder
-
-        Arguments:
-            dir_name {str} -- Target directory.
-
-        Returns:
-            {str} -- Path to the target directory.
-        """
-        test_dir = os.path.dirname(__file__)
-        dir_path = os.path.join(test_dir, dir_name)
-        return dir_path
+    def get_local_test_file(filepath: str) -> Path:
+        return Path(__file__).parent / TestUtils._name_local / filepath
 
     @staticmethod
-    def get_test_dir_output(dir_name: str) -> str:
-        """Returns the path to the output test data.
-        If it does not exist already it is created.
+    @contextlib.contextmanager
+    def working_directory(path: Path):
+        """Changes working directory and returns to previous on exit."""
+        prev_cwd = Path.cwd()
+        os.chdir(path)
+        try:
+            yield
+        finally:
+            os.chdir(prev_cwd)
 
-        Arguments:
-            dir_name {str} -- Name of the folder under Output.
 
-        Returns:
-            str -- Path to the test output dir.
-        """
-        output_dir = os.path.join('Output', dir_name)
-        test_dir = TestUtils.get_test_dir(output_dir)
-        # Create it if it does not exist
-        if not os.path.exists(test_dir):
-            os.mkdir(test_dir)
-        return test_dir
+skipwhenexternalsmissing = pytest.mark.skipif(
+    not (TestUtils.get_external_test_data_dir().is_dir()),
+    reason="Only to be run to generate expected data from local machines.",
+)
diff --git a/tests/test_Import.py b/tests/test_Import.py
index 77817ae1..a6a6475d 100644
--- a/tests/test_Import.py
+++ b/tests/test_Import.py
@@ -5,38 +5,37 @@
 import numbers
 from pathlib import Path
 import shutil
-from tests.TestUtils import TestUtils
+from tests.TestUtils import TestUtils, skipwhenexternalsmissing
 
 from fm2prof.Import import FmModelData, FMDataImporter
 
 
 class Test_FMDataImporter:
     @pytest.mark.unittest
+    @skipwhenexternalsmissing
     def test_when_map_file_without_czu_no_exception(self):
         # 1. Set up test data
-        test_map = Path(TestUtils.get_local_test_data_dir("main_test_data")).joinpath("fm_map.nc")
+        test_map = Path(TestUtils.get_local_test_data_dir("main_test_data")).joinpath(
+            "fm_map.nc"
+        )
+        assert test_map.is_file()
 
         # 2. Set initial expectations
+        return_value = FMDataImporter().import_dflow2d(test_map)
 
-        # 3. Run test
-        try:
-            FMDataImporter().import_dflow2d(test_map)
-        except:
-            pytest.fail('No exception expected but was thrown')
-        
-        # 4. Verify final expectations
-        
+        # 3. Verify final expectations
+        assert return_value is not None
 
-class Test_FmModelData:
 
+class Test_FmModelData:
     @pytest.mark.unittest
-    @pytest.mark.parametrize("arg_list", [(''), (None)])
+    @pytest.mark.parametrize("arg_list", [(""), (None)])
     def test_when_no_arguments_exception_is_risen(self, arg_list):
         # 1. Set up test data
         arg_list = arg_list
 
         # 2. Set initial expectations
-        expected_error_message = 'FM model data was not read correctly.'
+        expected_error_message = "FM model data was not read correctly."
 
         # 3. Run test
         with pytest.raises(Exception) as pytest_wrapped_e:
@@ -44,21 +43,26 @@ def test_when_no_arguments_exception_is_risen(self, arg_list):
 
         # 4. Verify final expectations
         recieved_error_message = str(pytest_wrapped_e.value)
-        assert expected_error_message == recieved_error_message, '' + \
-            'Expected error message {},'.format(expected_error_message) + \
-            ' does not match generated {}'.format(recieved_error_message)
+        assert expected_error_message == recieved_error_message, (
+            ""
+            + "Expected error message {},".format(expected_error_message)
+            + " does not match generated {}".format(recieved_error_message)
+        )
 
     @pytest.mark.unittest
-    @pytest.mark.parametrize("arg_list", [(''), (None)])
+    @pytest.mark.parametrize("arg_list", [(""), (None)])
     def test_when_argument_length_not_as_expected_then_exception_is_risen(
-            self, arg_list):
+        self, arg_list
+    ):
         # 1. Set up test data
-        arg_list = ['arg1', 'arg2']
+        arg_list = ["arg1", "arg2"]
 
         # 2. Set initial expectations
-        expected_error_message = '' + \
-            'Fm model data expects 5 arguments but only' + \
-            ' {} were given'.format(len(arg_list))
+        expected_error_message = (
+            ""
+            + "Fm model data expects 5 arguments but only"
+            + " {} were given".format(len(arg_list))
+        )
 
         # 3. Run test
         with pytest.raises(Exception) as pytest_wrapped_e:
@@ -66,36 +70,38 @@ def test_when_argument_length_not_as_expected_then_exception_is_risen(
 
         # 4. Verify final expectations
         recieved_error_message = str(pytest_wrapped_e.value)
-        assert expected_error_message == recieved_error_message, '' + \
-            'Expected error message {},'.format(expected_error_message) + \
-            ' does not match generated {}'.format(recieved_error_message)
+        assert expected_error_message == recieved_error_message, (
+            ""
+            + "Expected error message {},".format(expected_error_message)
+            + " does not match generated {}".format(recieved_error_message)
+        )
 
     @pytest.mark.unittest
     def test_when_given_expected_arguments_then_object_is_created(self):
         # 1. Set up test data
-        time_dependent_data = 'arg1'
-        time_independent_data = 'arg2'
-        edge_data = 'arg3'
-        node_coordinates = 'arg4'
-        css_data = 'arg5'
+        time_dependent_data = "arg1"
+        time_independent_data = "arg2"
+        edge_data = "arg3"
+        node_coordinates = "arg4"
+        css_data = "arg5"
         arg_list = [
             time_dependent_data,
             time_independent_data,
             edge_data,
             node_coordinates,
-            css_data]
+            css_data,
+        ]
         return_fm_model_data = None
         # 2. Run test
         try:
             return_fm_model_data = FmModelData(arg_list)
         except:
-            pytest.fail('No exception expected but was thrown')
+            pytest.fail("No exception expected but was thrown")
 
         # 4. Verify final expectations
         assert return_fm_model_data is not None
         assert return_fm_model_data.time_dependent_data == time_dependent_data
-        assert return_fm_model_data.time_independent_data \
-            == time_independent_data
+        assert return_fm_model_data.time_independent_data == time_independent_data
         assert return_fm_model_data.edge_data == edge_data
         assert return_fm_model_data.node_coordinates == node_coordinates
         assert return_fm_model_data.css_data_list == []
@@ -103,11 +109,11 @@ def test_when_given_expected_arguments_then_object_is_created(self):
     @pytest.mark.unittest
     def test_when_given_data_dictionary_then_css_data_list_is_set(self):
         # 1. Set up test data
-        time_dependent_data = 'arg1'
-        time_independent_data = 'arg2'
-        edge_data = 'arg3'
-        node_coordinates = 'arg4'
-        dummy_key = 'dummyKey'
+        time_dependent_data = "arg1"
+        time_independent_data = "arg2"
+        edge_data = "arg3"
+        node_coordinates = "arg4"
+        dummy_key = "dummyKey"
         dummy_values = [0, 1]
         css_data_dict = {
             dummy_key: dummy_values,
@@ -118,7 +124,8 @@ def test_when_given_data_dictionary_then_css_data_list_is_set(self):
             time_independent_data,
             edge_data,
             node_coordinates,
-            css_data_dict]
+            css_data_dict,
+        ]
         return_fm_model_data = None
 
         # 2. Set expectations
@@ -128,7 +135,7 @@ def test_when_given_data_dictionary_then_css_data_list_is_set(self):
         try:
             return_fm_model_data = FmModelData(arg_list)
         except:
-            pytest.fail('No exception expected but was thrown')
+            pytest.fail("No exception expected but was thrown")
 
         # 4. Verify final expectations
         assert return_fm_model_data is not None
@@ -137,12 +144,11 @@ def test_when_given_data_dictionary_then_css_data_list_is_set(self):
 
 
 class Test_get_ordered_css_list:
-
     @pytest.mark.unittest
     def test_when_given_dictionary_then_returns_list(self):
         # 1. Set up test_data
         return_list = None
-        dummy_key = 'dummyKey'
+        dummy_key = "dummyKey"
         dummy_values = [0, 1]
         test_dict = {
             dummy_key: dummy_values,
@@ -155,21 +161,22 @@ def test_when_given_dictionary_then_returns_list(self):
         try:
             return_list = FmModelData.get_ordered_css_list(test_dict)
         except:
-            pytest.fail('No exception expected but was thrown')
+            pytest.fail("No exception expected but was thrown")
 
         # 4. Verify final expectations
         assert return_list is not None
-        assert return_list == expected_list, '' + \
-            'Expected return value {},'.format(expected_list) + \
-            ' but return {} instead.'.format(return_list)
+        assert return_list == expected_list, (
+            ""
+            + "Expected return value {},".format(expected_list)
+            + " but return {} instead.".format(return_list)
+        )
 
     @pytest.mark.unittest
-    @pytest.mark.parametrize('test_dict', [(''), (None), ({})])
-    def test_when_given_unexpected_value_then_returns_empty_list(
-            self, test_dict):
+    @pytest.mark.parametrize("test_dict", [(""), (None), ({})])
+    def test_when_given_unexpected_value_then_returns_empty_list(self, test_dict):
         # 1. Set up test_data
         return_list = None
-        dummy_key = 'dummyKey'
+        dummy_key = "dummyKey"
         dummy_values = [0, 1]
 
         # 2. Run test
@@ -179,10 +186,12 @@ def test_when_given_unexpected_value_then_returns_empty_list(
         try:
             return_list = FmModelData.get_ordered_css_list(test_dict)
         except:
-            pytest.fail('No exception expected but was thrown')
+            pytest.fail("No exception expected but was thrown")
 
         # 4. Verify final expectations
         assert return_list is not None
-        assert return_list == expected_list, '' + \
-            'Expected return value {},'.format(expected_list) + \
-            ' but return {} instead.'.format(return_list)
+        assert return_list == expected_list, (
+            ""
+            + "Expected return value {},".format(expected_list)
+            + " but return {} instead.".format(return_list)
+        )
diff --git a/tests/test_acceptance.py b/tests/test_acceptance.py
index 9f897a51..99d24397 100644
--- a/tests/test_acceptance.py
+++ b/tests/test_acceptance.py
@@ -1,3 +1,4 @@
+from pathlib import Path
 import unittest
 import pytest
 import sys
@@ -6,7 +7,7 @@
 import shutil
 import matplotlib.pyplot as plt
 
-from tests.TestUtils import TestUtils
+from tests.TestUtils import TestUtils, skipwhenexternalsmissing
 from fm2prof.Fm2ProfRunner import Fm2ProfRunner
 from fm2prof.IniFile import IniFile
 
@@ -16,22 +17,23 @@
 from fm2prof.utils import VisualiseOutput
 from tests.fm2prof_latex_report import Fm2ProfLatexReport
 from tests.CompareWaalModel import CompareWaalModel as CompareWaalModel
-from tests.CompareIdealizedModel \
-    import CompareIdealizedModel, CompareHelper
+from tests.CompareIdealizedModel import CompareIdealizedModel, CompareHelper
+
+
 
 _root_output_dir = None
 
 # Test data to be used
-_waal_case = 'case_08_waal'
-_case01 = 'case_01_rectangle'
-_case02 = 'case_02_compound'
-_case03 = 'case_03_threestage'
-_case04 = 'case_04_storage'
-_case05 = 'case_05_dyke'
-_case06 = 'case_06_plassen'
-_case07 = 'case_07_triangular'
-_case09 = 'case_09_region_polygon'
-_case10 = 'case_10_section_polygon'
+_waal_case = "case_08_waal"
+_case01 = "case_01_rectangle"
+_case02 = "case_02_compound"
+_case03 = "case_03_threestage"
+_case04 = "case_04_storage"
+_case05 = "case_05_dyke"
+_case06 = "case_06_plassen"
+_case07 = "case_07_triangular"
+_case09 = "case_09_region_polygon"
+_case10 = "case_10_section_polygon"
 
 _test_scenarios_ids = [
     _case01,
@@ -43,7 +45,7 @@
     _case07,
     _case09,
     _case10,
-    _waal_case
+    _waal_case,
 ]
 
 """ To use excluding markups the following command line can be used:
@@ -56,69 +58,79 @@
 _test_scenarios = [
     pytest.param(
         _case01,
-        'Data\\2DModelOutput\\FlowFM_map.nc',
-        'Data\\cross_section_locations.xyz',
-        '',
-        ''),
+        "Data\\2DModelOutput\\FlowFM_map.nc",
+        "Data\\cross_section_locations.xyz",
+        "",
+        "",
+    ),
     pytest.param(
         _case02,
-        'Data\\2DModelOutput\\FlowFM_map.nc',
-        'Data\\cross_section_locations.xyz',
-        '',
-        ''),
+        "Data\\2DModelOutput\\FlowFM_map.nc",
+        "Data\\cross_section_locations.xyz",
+        "",
+        "",
+    ),
     pytest.param(
         _case03,
-        'Data\\2DModelOutput\\FlowFM_map.nc',
-        'Data\\cross_section_locations.xyz',
-        '',
-        ''),
+        "Data\\2DModelOutput\\FlowFM_map.nc",
+        "Data\\cross_section_locations.xyz",
+        "",
+        "",
+    ),
     pytest.param(
         _case04,
-        'Data\\2DmodelOutput\\FlowFM_map.nc',
-        'Data\\cross_section_locations.xyz',
-        '',
-        ''),
+        "Data\\2DmodelOutput\\FlowFM_map.nc",
+        "Data\\cross_section_locations.xyz",
+        "",
+        "",
+    ),
     pytest.param(
         _case05,
-        'Data\\2DmodelOutput\\FlowFM_map.nc',
-        'Data\\cross_section_locations.xyz',
-        '',
-        ''),
+        "Data\\2DmodelOutput\\FlowFM_map.nc",
+        "Data\\cross_section_locations.xyz",
+        "",
+        "",
+    ),
     pytest.param(
         _case06,
-        'Data\\2DmodelOutput\\FlowFM_map.nc',
-        'Data\\cross_section_locations.xyz',
-        '',
-        ''),
+        "Data\\2DmodelOutput\\FlowFM_map.nc",
+        "Data\\cross_section_locations.xyz",
+        "",
+        "",
+    ),
     pytest.param(
         _case07,
-        'Data\\2DModelOutput\\FlowFM_map.nc',
-        'Data\\cross_section_locations.xyz',
-        '',
-        ''),
+        "Data\\2DModelOutput\\FlowFM_map.nc",
+        "Data\\cross_section_locations.xyz",
+        "",
+        "",
+    ),
     pytest.param(
         _case09,
-        'Data\\FM\\FlowFM_fm2prof_map.nc',
-        'Data\\cross_section_locations.xyz',
-        'Data\\regions_complex.geojson',
-        ''),
+        "Data\\FM\\FlowFM_fm2prof_map.nc",
+        "Data\\cross_section_locations.xyz",
+        "Data\\regions_complex.geojson",
+        "",
+    ),
     pytest.param(
         _case10,
-        'Data\\FM\\FlowFM_fm2prof_map.nc',
-        'Data\\cross_section_locations.xyz',
-        '',
-        'Data\\sections_complex.geojson'),
+        "Data\\FM\\FlowFM_fm2prof_map.nc",
+        "Data\\cross_section_locations.xyz",
+        "",
+        "Data\\sections_complex.geojson",
+    ),
     pytest.param(
         _waal_case,
-        'Data\\FM\\FlowFM_fm2prof_map.nc',
-        'Data\\cross_section_locations.xyz',
-        '',
-        '',
-        marks=pytest.mark.slow)
+        "Data\\FM\\FlowFM_fm2prof_map.nc",
+        "Data\\cross_section_locations.xyz",
+        "",
+        "",
+        marks=pytest.mark.slow,
+    ),
 ]
 
-_run_with_files_dir_name = 'RunWithFiles_Output'
-_base_output_dir_name = 'Output'
+_run_with_files_dir_name = "RunWithFiles_Output"
+_base_output_dir_name = "Output"
 
 
 def get_valid_inifile_input_parameters():
@@ -134,35 +146,34 @@ def get_valid_inifile_input_parameters():
         "sdstorage": 1,
         "frictionweighing": 0,
         "sectionsmethod": 0,
-        "exportmapfiles": 0
+        "exportmapfiles": 0,
     }
 
 
-def _get_base_output_dir():
+def _get_base_output_dir() -> Path:
     """
     Sets up the necessary data for MainMethodTest
     """
     output_dir = _create_test_root_output_dir(_run_with_files_dir_name)
     # Create it if it does not exist
-    if not os.path.exists(output_dir):
-        os.mkdir(output_dir)
+    if not output_dir.is_dir():
+        output_dir.mkdir()
     return output_dir
 
 
-def _create_test_root_output_dir(dirName=None):
+def _create_test_root_output_dir(dirName=None) -> Path:
     """
     Create test output directory
     so it's easier to collect output afterwards.
     """
-    _root_output_dir = os.path.join(
-        os.path.dirname(__file__), _base_output_dir_name)
-    if not os.path.exists(_root_output_dir):
-        os.mkdir(_root_output_dir)
+    _root_output_dir = Path(__file__).parent / _base_output_dir_name
+    if not _root_output_dir.is_dir():
+        _root_output_dir.mkdir()
 
     if dirName is not None:
-        subOutputDir = os.path.join(_root_output_dir, dirName)
-        if not os.path.exists(subOutputDir):
-            os.mkdir(subOutputDir)
+        subOutputDir: Path = _root_output_dir / dirName
+        if not subOutputDir.is_dir():
+            subOutputDir.mkdir()
         return subOutputDir
 
     return _root_output_dir
@@ -179,71 +190,59 @@ def _check_and_create_test_case_output_dir(base_output_dir, caseName):
     if os.path.exists(output_directory) and os.listdir(output_directory):
         shutil.rmtree(output_directory)
 
-    #if not os.path.exists(output_directory):
+    # if not os.path.exists(output_directory):
     #    os.mkdir(output_directory)
 
     return output_directory
-    
 
 
-def _get_test_case_output_dir(case_name: str):
+def _get_test_case_output_dir(case_name: str) -> Path:
     base_output_dir = _get_base_output_dir()
-    output_directory = os.path.join(base_output_dir, case_name, 'CaseName01')
+    output_directory = base_output_dir / case_name / "CaseName01"
     return output_directory
 
 
 class ARCHIVED_Test_Generate_Reports:
     _latex_report_path = None
 
-    @pytest.fixture(scope='class')
+    @pytest.fixture(scope="class")
     def report_data(self):
-        """Prepares the class properties to be used in the tests.
-        """
-        test_data_dir = os.path.join(
-            _base_output_dir_name, _run_with_files_dir_name)
+        """Prepares the class properties to be used in the tests."""
+        test_data_dir = os.path.join(_base_output_dir_name, _run_with_files_dir_name)
         test_data_dir_path = TestUtils.get_test_dir(test_data_dir)
         report_content = Fm2ProfLatexReport(
-            scenarios_ids=_test_scenarios_ids,
-            data_dir=test_data_dir_path)
+            scenarios_ids=_test_scenarios_ids, data_dir=test_data_dir_path
+        )
         yield test_data_dir_path, report_content
 
     @pytest.mark.generate_test_report
-    def test_when_output_generated_then_generate_latex_source_file(
-            self, report_data):
+    def test_when_output_generated_then_generate_latex_source_file(self, report_data):
 
-        assert report_data is not None, '' + \
-            'No test data available.'
+        assert report_data is not None, "" + "No test data available."
 
         # We save the generated report in the test directory as well.
         test_data_dir, report_content = report_data
         output_dir = test_data_dir
         try:
             report = LatexReport(report_content)
-            latex_report_path = \
-                report.generate_latex_report(
-                    target_dir=output_dir)
+            latex_report_path = report.generate_latex_report(target_dir=output_dir)
             assert os.path.exists(latex_report_path)
         except Exception as e_info:
-            err_mssg = 'Error while generating latex source ' + \
-                '{}'.format(str(e_info))
+            err_mssg = "Error while generating latex source " + "{}".format(str(e_info))
             pytest.fail(err_mssg)
 
     @pytest.mark.generate_test_report
     def test_when_latex_source_generated_then_compile_to_pdf(self):
         try:
-            LatexReport.convert_to_pdf(
-                'tests/Output/RunWithFiles_Output/latex_report/')
+            LatexReport.convert_to_pdf("tests/Output/RunWithFiles_Output/latex_report/")
         except Exception as e_info:
-            err_mssg = 'Error while compiling latex report ' + \
-                '{}'.format(str(e_info))
+            err_mssg = "Error while compiling latex report " + "{}".format(str(e_info))
             pytest.fail(err_mssg)
 
     @pytest.mark.generate_test_report
-    def test_when_output_generated_then_generate_html_report(
-            self, report_data):
+    def test_when_output_generated_then_generate_html_report(self, report_data):
 
-        assert report_data is not None, '' + \
-            'No test data available.'
+        assert report_data is not None, "" + "No test data available."
 
         # We save the generated report in the test directory as well.
         test_data_dir, report_content = report_data
@@ -252,27 +251,32 @@ def test_when_output_generated_then_generate_html_report(
             report = HtmlReport(report_content)
             report.generate_html_report(target_dir=output_dir)
         except Exception as e_info:
-            err_mssg = 'Error while generating python report ' + \
-                '{}'.format(str(e_info))
+            err_mssg = "Error while generating python report " + "{}".format(
+                str(e_info)
+            )
             pytest.fail(err_mssg)
 
 
 class Test_Run_Testcases:
-
     @pytest.mark.acceptance
     @pytest.mark.parametrize(
         ("case_name", "map_file", "css_file", "region_file", "section_file"),
-        _test_scenarios[:-3], ids=_test_scenarios_ids[:-3])
+        _test_scenarios[:-3],
+        ids=_test_scenarios_ids[:-3],
+    )
+    @skipwhenexternalsmissing
     def test_when_given_input_data_then_output_is_generated(
-            self, case_name, map_file, css_file, region_file, section_file):
+        self, case_name, map_file, css_file, region_file, section_file
+    ):
         # 1. Set up test data.
         iniFilePath = None
         iniFile = IniFile(iniFilePath)
         test_data_dir = TestUtils.get_external_test_data_dir(case_name)
         base_output_dir = _get_base_output_dir()
 
-        iniFile._set_output_directory_no_validation(_check_and_create_test_case_output_dir(
-            base_output_dir, case_name))
+        iniFile._set_output_directory_no_validation(
+            _check_and_create_test_case_output_dir(base_output_dir, case_name)
+        )
 
         if region_file:
             region_file_path = os.path.join(test_data_dir, region_file)
@@ -284,48 +288,52 @@ def test_when_given_input_data_then_output_is_generated(
         else:
             section_file_path = section_file
 
-        #iniFile.set_parameter('ExportMapFiles', True)
-        iniFile.set_parameter('skipmaps', 6)
-        iniFile.set_input_file('2dmapoutput', os.path.join(test_data_dir, map_file))
-        iniFile.set_input_file('crosssectionlocationfile', os.path.join(test_data_dir, css_file))
-        iniFile.set_input_file('regionpolygonfile', region_file_path)
-        iniFile.set_input_file('sectionpolygonfile', section_file_path)
+        # iniFile.set_parameter('ExportMapFiles', True)
+        iniFile.set_parameter("skipmaps", 6)
+        iniFile.set_input_file("2dmapoutput", os.path.join(test_data_dir, map_file))
+        iniFile.set_input_file(
+            "crosssectionlocationfile", os.path.join(test_data_dir, css_file)
+        )
+        iniFile.set_input_file("regionpolygonfile", region_file_path)
+        iniFile.set_input_file("sectionpolygonfile", section_file_path)
 
         # Create the runner and set the saving figures variable to true
         buf = io.StringIO(iniFile.print_configuration())
         runner = Fm2ProfRunner(buf)
 
         # 2. Verify precondition (no output generated)
-        assert (os.path.exists(iniFile.get_output_directory()) and
-                not len(os.listdir(iniFile.get_output_directory())) > 1)
+        assert (
+            os.path.exists(iniFile.get_output_directory())
+            and not len(os.listdir(iniFile.get_output_directory())) > 1
+        )
 
         # 3. Run file:
         runner.run()
 
         # 4. Verify there is output generated:
-        assert os.listdir(iniFile.get_output_directory()), '' + \
-            'There is no output generated for {0}'.format(case_name)
+        assert os.listdir(
+            iniFile.get_output_directory()
+        ), "" + "There is no output generated for {0}".format(case_name)
 
 
 class ARCHIVED_Test_Main_Run_IniFile:
-
     def __run_main_with_arguments(self, ini_file):
         pythonCall = "fm2prof\\main.py -i {0}".format(ini_file)
         os.system("python {0}".format(pythonCall))
 
     def __create_test_ini_file(self, root_dir, case_name, map_file, css_file):
-        output_dir = os.path.join(root_dir, 'OutputFiles')
+        output_dir = os.path.join(root_dir, "OutputFiles")
         if not os.path.exists(output_dir):
             os.makedirs(output_dir)
 
-        input_files_key = 'InputFiles'
-        input_parameters_key = 'InputParameters'
-        output_directory_key = 'OutputDirectory'
+        input_files_key = "InputFiles"
+        input_parameters_key = "InputParameters"
+        output_directory_key = "OutputDirectory"
 
-        test_data_dir = TestUtils.get_local_test_data_dir('main_test_data')
+        test_data_dir = TestUtils.get_local_test_data_dir("main_test_data")
         input_file_paths = {
             "fm_netcdfile": os.path.join(test_data_dir, map_file),
-            'crosssectionlocationfile': os.path.join(test_data_dir, css_file),
+            "crosssectionlocationfile": os.path.join(test_data_dir, css_file),
         }
         input_parameters = {
             "number_of_css_points": 20,
@@ -340,25 +348,25 @@ def __create_test_ini_file(self, root_dir, case_name, map_file, css_file):
             "frictionweighing": 0,
             "sectionsmethod": 0,
             "sdoptimisationmethod": 0,
-            "exportmapfiles": 0
+            "exportmapfiles": 0,
         }
 
         # write file
-        file_path = os.path.join(root_dir, '{}_ini_file.ini'.format(case_name))
-        f = open(file_path, 'w+')
+        file_path = os.path.join(root_dir, "{}_ini_file.ini".format(case_name))
+        f = open(file_path, "w+")
 
-        f.writelines('[{}]\r\n'.format(input_files_key))
+        f.writelines("[{}]\r\n".format(input_files_key))
         for key, value in input_file_paths.items():
-            f.writelines('{} = {}\r\n'.format(key, value))
-        f.writelines('\r\n')
-        f.writelines('[{}]\r\n'.format(input_parameters_key))
+            f.writelines("{} = {}\r\n".format(key, value))
+        f.writelines("\r\n")
+        f.writelines("[{}]\r\n".format(input_parameters_key))
         for key, value in input_parameters.items():
-            f.writelines('{} = {}\r\n'.format(key, value))
+            f.writelines("{} = {}\r\n".format(key, value))
 
-        f.writelines('\r\n')
-        f.writelines('[{}]\r\n'.format(output_directory_key))
-        f.writelines('OutputDir = {}\r\n'.format(output_dir))
-        f.writelines('CaseName = {}\r\n'.format(case_name))
+        f.writelines("\r\n")
+        f.writelines("[{}]\r\n".format(output_directory_key))
+        f.writelines("OutputDir = {}\r\n".format(output_dir))
+        f.writelines("CaseName = {}\r\n".format(case_name))
 
         f.close()
         return (file_path, output_dir)
@@ -376,21 +384,22 @@ def _get_custom_dir(self):
     @pytest.mark.systemtest
     def test_when_given_inifile_then_output_is_generated(self):
         # 1. Set up test data.
-        case_name = 'main_case'
-        map_file = 'fm_map.nc'
-        css_file = 'fm_css.xyz'
+        case_name = "main_case"
+        map_file = "fm_map.nc"
+        css_file = "fm_css.xyz"
         root_output_dir = self._get_custom_dir()
         (ini_file_path, output_dir) = self.__create_test_ini_file(
-            root_output_dir, case_name, map_file, css_file)
+            root_output_dir, case_name, map_file, css_file
+        )
 
         # 2. Verify precondition (no output generated)
         assert os.path.exists(ini_file_path)
         expected_files = [
-            'CrossSectionDefinitions.ini',
-            'CrossSectionLocations.ini',
-            'geometry.csv',
-            'roughness.csv',
-            'volumes.csv',
+            "CrossSectionDefinitions.ini",
+            "CrossSectionLocations.ini",
+            "geometry.csv",
+            "roughness.csv",
+            "volumes.csv",
         ]
 
         # 3. Run file:
@@ -399,24 +408,22 @@ def test_when_given_inifile_then_output_is_generated(self):
         except Exception as e_error:
             if os.path.exists(root_output_dir):
                 shutil.rmtree(root_output_dir)
-            pytest.fail(
-                'No exception expected but was thrown {}.'.format(
-                    str(e_error)))
+            pytest.fail("No exception expected but was thrown {}.".format(str(e_error)))
 
         # 4. Verify there is output generated:
-        output_files = os.path.join(output_dir, '{}01'.format(case_name))
+        output_files = os.path.join(output_dir, "{}01".format(case_name))
         generated_files = os.listdir(output_files)
         if os.path.exists(root_output_dir):
             shutil.rmtree(root_output_dir)
-        assert generated_files, '' + \
-            'There is no output generated for {0}'.format(case_name)
+        assert generated_files, "" + "There is no output generated for {0}".format(
+            case_name
+        )
         for expected_file in expected_files:
             assert expected_file in generated_files
 
 
 class ARCHIVED_Test_Compare_Waal_Model:
-    """Requires fm2prof output generated for waal_case
-    """
+    """Requires fm2prof output generated for waal_case"""
 
     @pytest.mark.slow
     @pytest.mark.acceptance
@@ -424,8 +431,8 @@ class ARCHIVED_Test_Compare_Waal_Model:
     def test_when_fm2prof_output_then_use_it_for_sobek_model_input(self):
         # 1. Set up test data
         waal_test_folder = TestUtils.get_external_test_data_dir(_waal_case)
-        sobek_dir = os.path.join(waal_test_folder, 'Model_SOBEK')
-        fm_dir = os.path.join(waal_test_folder, 'Model_FM')
+        sobek_dir = os.path.join(waal_test_folder, "Model_SOBEK")
+        fm_dir = os.path.join(waal_test_folder, "Model_FM")
         fm2prof_dir = _get_test_case_output_dir(_waal_case)
 
         result_figures = []
@@ -437,22 +444,24 @@ def test_when_fm2prof_output_then_use_it_for_sobek_model_input(self):
                 case_name=_waal_case,
                 results_dir=fm2prof_dir,
                 sobek_dir=sobek_dir,
-                fm_dir=fm_dir)
+                fm_dir=fm_dir,
+            )
         except Exception as e_info:
             pytest.fail(
-                'No exception expected but was thrown ' +
-                '{}.'.format(str(e_info)))
+                "No exception expected but was thrown " + "{}.".format(str(e_info))
+            )
 
         # 3. Verify final expectations
         assert output_1d
-        assert os.path.exists(output_1d), '' + \
-                'No output found at {}.'.format(output_1d)
+        assert os.path.exists(output_1d), "" + "No output found at {}.".format(
+            output_1d
+        )
 
     def test_when_sobek_output_exist_then_create_figures(self):
         # 1. Set up test data
         waal_test_folder = TestUtils.get_external_test_data_dir(_waal_case)
-        sobek_dir = os.path.join(waal_test_folder, 'Model_SOBEK')
-        fm_dir = os.path.join(waal_test_folder, 'Model_FM')
+        sobek_dir = os.path.join(waal_test_folder, "Model_SOBEK")
+        fm_dir = os.path.join(waal_test_folder, "Model_FM")
         fm2prof_dir = _get_test_case_output_dir(_waal_case)
 
         result_figures = []
@@ -464,24 +473,26 @@ def test_when_sobek_output_exist_then_create_figures(self):
                 case_name=_waal_case,
                 results_dir=fm2prof_dir,
                 sobek_dir=sobek_dir,
-                fm_dir=fm_dir)
+                fm_dir=fm_dir,
+            )
         except Exception as e_info:
             pytest.fail(
-                'No exception expected but was thrown ' +
-                '{}.'.format(str(e_info)))
+                "No exception expected but was thrown " + "{}.".format(str(e_info))
+            )
 
         # 3. Verify final expectations
         assert result_figures
         for fig_path in result_figures:
-            assert os.path.exists(fig_path), '' + \
-                'Figure not found at path {}.'.format(fig_path)
+            assert os.path.exists(fig_path), "" + "Figure not found at path {}.".format(
+                fig_path
+            )
 
     @pytest.mark.acceptance
     @pytest.mark.requires_output
     @pytest.mark.parametrize(
-        ("case_name"), _test_scenarios_ids, ids=_test_scenarios_ids)
-    def test_when_output_exists_then_compare_waal_model_volume(
-            self, case_name: str):
+        ("case_name"), _test_scenarios_ids, ids=_test_scenarios_ids
+    )
+    def test_when_output_exists_then_compare_waal_model_volume(self, case_name: str):
         if case_name != _waal_case:
             # print('This case is tested on another fixture.')
             return
@@ -489,74 +500,78 @@ def test_when_output_exists_then_compare_waal_model_volume(
         fm2prof_dir = _get_test_case_output_dir(case_name)
         # Data from the above tests is saved directly in fm2prof_dir,
         # not in case_name/output
-        fm2prof_fig_dir = os.path.join(fm2prof_dir, 'Figures')
+        fm2prof_fig_dir = os.path.join(fm2prof_dir, "Figures")
 
-        volume_file_name = 'volumes.csv'
+        volume_file_name = "volumes.csv"
         input_volume_file = os.path.join(fm2prof_dir, volume_file_name)
 
         # 2. Verify / create necessary folders and directories
-        assert os.path.exists(input_volume_file), '' + \
-            'Input file {} could not be found'.format(input_volume_file)
+        assert os.path.exists(
+            input_volume_file
+        ), "" + "Input file {} could not be found".format(input_volume_file)
         if not os.path.exists(fm2prof_fig_dir):
             os.makedirs(fm2prof_fig_dir)
 
         #  3. Run
         try:
             waal_comparer = CompareWaalModel()
-            waal_comparer._compare_volume(
-                    case_name, input_volume_file, fm2prof_fig_dir)
+            waal_comparer._compare_volume(case_name, input_volume_file, fm2prof_fig_dir)
         except Exception as e_info:
             pytest.fail(
-                'No exception expected but was thrown ' +
-                '{}.'.format(str(e_info)))
+                "No exception expected but was thrown " + "{}.".format(str(e_info))
+            )
 
         #  4. Final expectation
-        assert os.listdir(fm2prof_fig_dir), '' + \
-            'There is no volume output generated for {0}'.format(case_name)
+        assert os.listdir(
+            fm2prof_fig_dir
+        ), "" + "There is no volume output generated for {0}".format(case_name)
 
 
 class Test_Compare_Idealized_Model:
     # region of helpers
     __case_01_tzw = [
         [0, 150, 0],
-        [0, 150+1e-5, 0+1e-5],
+        [0, 150 + 1e-5, 0 + 1e-5],
+        [3000, 150, -1],
         [3000, 150, -1],
-        [3000, 150, -1]]
+    ]
 
     __case_02_tzw = [
         [0, 0, -2],
-        [0, 50-1e-2, -2],
+        [0, 50 - 1e-2, -2],
         [0, 50, 0],
         [0, 150, 1e-2],
         [3000, 0, -3],
-        [3000, 50-1e-2, -3],
+        [3000, 50 - 1e-2, -3],
         [3000, 50, -1],
-        [3000, 150, -1+1e-2]]
+        [3000, 150, -1 + 1e-2],
+    ]
 
     __case_03_tzw = [
         [0, 0, -2],
-        [0, 50-1e-2, -2],
+        [0, 50 - 1e-2, -2],
         [0, 50, 0],
-        [0, 100-1e-2, 0],
+        [0, 100 - 1e-2, 0],
         [0, 100, 0.5],
         [0, 150, 0.5],
         [3000, 0, -3],
-        [3000, 50-1e-2, -3],
+        [3000, 50 - 1e-2, -3],
         [3000, 50, -1],
-        [3000, 100-1e-2, -1],
+        [3000, 100 - 1e-2, -1],
         [3000, 100, -0.5],
         [3000, 150, -0.5],
-       ]
+    ]
 
     __case_05_tzw = [
         [0, 0, -2],
-        [0, 50-1e-2, -2],
+        [0, 50 - 1e-2, -2],
         [0, 50, 1],
-        [0, 150, 1+1e-2],
+        [0, 150, 1 + 1e-2],
         [3000, 0, -3],
-        [3000, 50-1e-2, -3],
+        [3000, 50 - 1e-2, -3],
         [3000, 50, 0],
-        [3000, 150, 0+1e-2]]
+        [3000, 150, 0 + 1e-2],
+    ]
 
     __case_07_tzw = [
         [0, 00, -2],
@@ -566,7 +581,8 @@ class Test_Compare_Idealized_Model:
         [10000, 00, -4],
         [10000, 200, -4],
         [10000, 200.000001, -2],
-        [10000, 500, -2]]
+        [10000, 500, -2],
+    ]
 
     __case_tzw_dict = {
         _case01: __case_01_tzw,
@@ -584,9 +600,9 @@ class Test_Compare_Idealized_Model:
     @pytest.mark.acceptance
     @pytest.mark.requires_output
     @pytest.mark.parametrize(
-        ("case_name"), _test_scenarios_ids, ids=_test_scenarios_ids)
-    def ARCHIVED_test_compare_generic_model_geometry(
-            self, case_name: str):
+        ("case_name"), _test_scenarios_ids, ids=_test_scenarios_ids
+    )
+    def ARCHIVED_test_compare_generic_model_geometry(self, case_name: str):
         if case_name == _waal_case:
             # print('This case is tested on another fixture.')
             return
@@ -594,90 +610,95 @@ def ARCHIVED_test_compare_generic_model_geometry(
         fm2prof_dir = _get_test_case_output_dir(case_name)
         # Data from the above tests is saved directly in fm2prof_dir,
         # not in case_name/output
-        fm2prof_fig_dir_head = os.path.join(fm2prof_dir, 'Figures')
-        fm2prof_fig_dir = os.path.join(fm2prof_fig_dir_head, 'Geometry')
+        fm2prof_fig_dir_head = os.path.join(fm2prof_dir, "Figures")
+        fm2prof_fig_dir = os.path.join(fm2prof_fig_dir_head, "Geometry")
 
-        geometry_file_name = 'geometry.csv'
+        geometry_file_name = "geometry.csv"
         input_geometry_file = os.path.join(fm2prof_dir, geometry_file_name)
 
         # 2. Verify / create necessary folders and directories
-        assert os.path.exists(input_geometry_file), '' + \
-            'Input file {} could not be found'.format(input_geometry_file)
+        assert os.path.exists(
+            input_geometry_file
+        ), "" + "Input file {} could not be found".format(input_geometry_file)
 
         if os.path.exists(fm2prof_fig_dir):
             shutil.rmtree(fm2prof_fig_dir)
         os.makedirs(fm2prof_fig_dir)
-        #os.makedirs(fm2prof_fig_dir)
+        # os.makedirs(fm2prof_fig_dir)
 
         #  3. Run
         tzw_values = self.__case_tzw_dict.get(case_name)
         if not tzw_values or tzw_values is None:
-            pytest.fail(
-                'Test failed, no values retrieved for {}'.format(case_name))
+            pytest.fail("Test failed, no values retrieved for {}".format(case_name))
 
         try:
             generic_comparer = CompareIdealizedModel()
             generic_comparer._compare_css(
-                    case_name, tzw_values,
-                    input_geometry_file, fm2prof_fig_dir)
+                case_name, tzw_values, input_geometry_file, fm2prof_fig_dir
+            )
         except Exception as e_info:
             pytest.fail(
-                'No exception expected but was thrown ' +
-                '{}.'.format(str(e_info)))
+                "No exception expected but was thrown " + "{}.".format(str(e_info))
+            )
 
         #  4. Final expectation
-        assert os.listdir(fm2prof_fig_dir), '' + \
-            'There is no geometry output generated for {0}'.format(case_name)
+        assert os.listdir(
+            fm2prof_fig_dir
+        ), "" + "There is no geometry output generated for {0}".format(case_name)
 
     # region for tests
     @pytest.mark.acceptance
     @pytest.mark.requires_output
     @pytest.mark.parametrize(
-        ("case_name"), _test_scenarios_ids, ids=_test_scenarios_ids)
+        ("case_name"), _test_scenarios_ids, ids=_test_scenarios_ids
+    )
     def ARCHIVED_test_when_output_exists_then_compare_generic_model_roughness(
-            self, case_name: str):
+        self, case_name: str
+    ):
         if case_name == _waal_case:
             # print('This case is tested on another fixture.')
             return
         # 1. Get all necessary output / input directories
         fm2prof_dir = _get_test_case_output_dir(case_name)
-        fm2prof_fig_dir = os.path.join(fm2prof_dir, 'Figures', 'Roughness')
+        fm2prof_fig_dir = os.path.join(fm2prof_dir, "Figures", "Roughness")
 
-        roughness_file_name = 'roughness.csv'
-        input_roughness_file = os.path.join(
-            fm2prof_dir, roughness_file_name)
+        roughness_file_name = "roughness.csv"
+        input_roughness_file = os.path.join(fm2prof_dir, roughness_file_name)
 
         # 2. Verify / create necessary folders and directories
-        assert os.path.exists(input_roughness_file), '' + \
-            'Input file {} could not be found'.format(input_roughness_file)
+        assert os.path.exists(
+            input_roughness_file
+        ), "" + "Input file {} could not be found".format(input_roughness_file)
         if not os.path.exists(fm2prof_fig_dir):
             os.makedirs(fm2prof_fig_dir)
 
         #  3. Run
         tzw_values = self.__case_tzw_dict.get(case_name)
         if not tzw_values or tzw_values is None:
-            pytest.fail(
-                'Test failed, no values retrieved for {}'.format(case_name))
+            pytest.fail("Test failed, no values retrieved for {}".format(case_name))
 
         try:
             generic_comparer = CompareIdealizedModel()
             generic_comparer._compare_roughness(
-                    case_name, tzw_values,
-                    input_roughness_file, fm2prof_fig_dir)
+                case_name, tzw_values, input_roughness_file, fm2prof_fig_dir
+            )
         except Exception as e_info:
             pytest.fail(
-                'No exception expected but was thrown ' +
-                '{}.'.format(str(e_info)))
+                "No exception expected but was thrown " + "{}.".format(str(e_info))
+            )
 
-        assert os.listdir(fm2prof_fig_dir), '' + \
-            'There is no roughness output generated for {0}'.format(case_name)
+        assert os.listdir(
+            fm2prof_fig_dir
+        ), "" + "There is no roughness output generated for {0}".format(case_name)
 
     @pytest.mark.acceptance
     @pytest.mark.requires_output
     @pytest.mark.parametrize(
-        ("case_name"), _test_scenarios_ids, ids=_test_scenarios_ids)
+        ("case_name"), _test_scenarios_ids, ids=_test_scenarios_ids
+    )
     def ARCHIVED_test_when_output_exists_then_compare_generic_model_volume(
-            self, case_name: str):
+        self, case_name: str
+    ):
         if case_name == _waal_case:
             # print('This case is tested on another fixture.')
             return
@@ -685,14 +706,15 @@ def ARCHIVED_test_when_output_exists_then_compare_generic_model_volume(
         fm2prof_dir = _get_test_case_output_dir(case_name)
         # Data from the above tests is saved directly in fm2prof_dir,
         # not in case_name/output
-        fm2prof_fig_dir = os.path.join(fm2prof_dir, 'Figures', 'Volume')
+        fm2prof_fig_dir = os.path.join(fm2prof_dir, "Figures", "Volume")
 
-        volume_file_name = 'volumes.csv'
+        volume_file_name = "volumes.csv"
         input_volume_file = os.path.join(fm2prof_dir, volume_file_name)
 
         # 2. Verify / create necessary folders and directories
-        assert os.path.exists(input_volume_file), '' + \
-            'Input file {} could not be found'.format(input_volume_file)
+        assert os.path.exists(
+            input_volume_file
+        ), "" + "Input file {} could not be found".format(input_volume_file)
         if not os.path.exists(fm2prof_fig_dir):
             os.makedirs(fm2prof_fig_dir)
 
@@ -700,74 +722,76 @@ def ARCHIVED_test_when_output_exists_then_compare_generic_model_volume(
         try:
             generic_comparer = CompareIdealizedModel()
             generic_comparer._compare_volume(
-                    case_name, input_volume_file, fm2prof_fig_dir)
+                case_name, input_volume_file, fm2prof_fig_dir
+            )
         except Exception as e_info:
             pytest.fail(
-                'No exception expected but was thrown ' +
-                '{}.'.format(str(e_info)))
+                "No exception expected but was thrown " + "{}.".format(str(e_info))
+            )
 
         #  4. Final expectation
-        assert os.listdir(fm2prof_fig_dir), '' + \
-            'There is no volume output generated for {0}'.format(case_name)
+        assert os.listdir(
+            fm2prof_fig_dir
+        ), "" + "There is no volume output generated for {0}".format(case_name)
 
     @pytest.mark.acceptance
-    @pytest.mark.requires_output
     @pytest.mark.parametrize(
-        ("case_name"), _test_scenarios_ids[:-3], ids=_test_scenarios_ids[:-3])
+        ("case_name"), _test_scenarios_ids[:-3], ids=_test_scenarios_ids[:-3]
+    )
+    @skipwhenexternalsmissing
     def test_when_output_exists_then_compare_with_reference(self, case_name: str):
         """
         This test is supposed to supercede the others
         """
         # 1. Get all necessary output / input directories
         reference_geometry = self.__case_tzw_dict.get(case_name)
-        reference_roughness = None#CompareHelper.get_analytical_roughness_for_case(case_name)
+        reference_roughness = (
+            None  # CompareHelper.get_analytical_roughness_for_case(case_name)
+        )
         reference__volume = []
         fm2prof_dir = _get_test_case_output_dir(case_name)
 
         # 2. Verify / create necessary folders and directories
         #  3. Run
-        
+
         visualiser = VisualiseOutput(fm2prof_dir)
         frictionhelper = CompareHelper.get_analytical_roughness_for_case(case_name)
         for css in visualiser.cross_sections():
             ref = CompareHelper.interpolate_to_css(css, reference_geometry)
             ref = CompareHelper.convert_ZW_to_symmetric_css(ref)
-            
+
             ref_friction = frictionhelper(css)
-            visualiser.make_figure(css, reference_geometry=ref, reference_roughness=ref_friction)
+            visualiser.make_figure(
+                css, reference_geometry=ref, reference_roughness=ref_friction
+            )
 
 
 class ARCHIVED_Test_WaalPerformance:
-
     @pytest.mark.acceptance
     @pytest.mark.workinprogress
     def test_when_waal_case_then_performance_is_slow(self):
         # 1. Set up test model.
-        case_name = 'case_08_waal'
-        local_test_dir = TestUtils.get_local_test_data_dir('performance_waal')
-        ini_file = os.path.join(local_test_dir, 'fm2prof_08.ini')
-        json_file = \
-            os.path.join(local_test_dir, 'SectionPolygonDissolved.json')
+        case_name = "case_08_waal"
+        local_test_dir = TestUtils.get_local_test_data_dir("performance_waal")
+        ini_file = os.path.join(local_test_dir, "fm2prof_08.ini")
+        json_file = os.path.join(local_test_dir, "SectionPolygonDissolved.json")
         external_test_dir = TestUtils.get_external_test_data_dir(case_name)
-        map_file = os.path.join(
-            external_test_dir,
-            'Data\\FM\\FlowFM_fm2prof_map.nc')
-        css_file = os.path.join(
-            external_test_dir,
-            'Data\\cross_section_locations.xyz')
+        map_file = os.path.join(external_test_dir, "Data\\FM\\FlowFM_fm2prof_map.nc")
+        css_file = os.path.join(external_test_dir, "Data\\cross_section_locations.xyz")
 
         # 1.1. Create ini file.
         ini_file_path = None
         test_ini_file = IniFile(ini_file_path)
         base_output_dir = _get_base_output_dir()
-        test_ini_file._output_dir = \
-            _check_and_create_test_case_output_dir(base_output_dir, case_name)
+        test_ini_file._output_dir = _check_and_create_test_case_output_dir(
+            base_output_dir, case_name
+        )
 
         test_ini_file._input_file_paths = {
-            'fm_netcdfile': map_file,
-            'crosssectionlocationfile': css_file,
-            'regionpolygonfile': None,
-            'sectionpolygonfile': json_file
+            "fm_netcdfile": map_file,
+            "crosssectionlocationfile": css_file,
+            "regionpolygonfile": None,
+            "sectionpolygonfile": json_file,
         }
         test_ini_file._input_parameters = {
             "number_of_css_points": 20,
@@ -782,15 +806,14 @@ def test_when_waal_case_then_performance_is_slow(self):
             "frictionweighing": 0,
             "sectionsmethod": 1,
             "sdoptimisationmethod": 0,
-            "exportmapfiles": 1
+            "exportmapfiles": 1,
         }
 
         # 2. Verify initial expectations.
-        assert os.path.exists(ini_file), 'Ini (test) file was not found.'
-        assert os.path.exists(json_file), 'Json (test) file was not found.'
-        assert os.path.exists(map_file), 'Map (test) file was not found.'
-        assert os.path.exists(css_file), '' + \
-            'CrossSection (test) file was not found'
+        assert os.path.exists(ini_file), "Ini (test) file was not found."
+        assert os.path.exists(json_file), "Json (test) file was not found."
+        assert os.path.exists(map_file), "Map (test) file was not found."
+        assert os.path.exists(css_file), "" + "CrossSection (test) file was not found"
 
         # 3. Run test.
         try:
@@ -799,9 +822,7 @@ def test_when_waal_case_then_performance_is_slow(self):
         except Exception as e_error:
             # if os.path.exists(root_output_dir):
             #     shutil.rmtree(root_output_dir)
-            pytest.fail(
-                'No exception expected but was thrown {}.'.format(
-                    str(e_error)))
+            pytest.fail("No exception expected but was thrown {}.".format(str(e_error)))
 
         # 4. Verify final expectations.
         pass
@@ -810,7 +831,7 @@ def test_dummy_timing(self):
         import timeit
 
         def f():
-            y = next((i for i in range(100000) if i == 1000), '-10')
+            y = next((i for i in range(100000) if i == 1000), "-10")
             print(y)
 
         def fs():
@@ -822,13 +843,14 @@ def fs():
         assert f_res < fs_res
 
     def merge_names(self, a, b):
-        val = '{} & {}'.format(a, b)
+        val = "{} & {}".format(a, b)
         return val
 
     def test_dummy_mp(self):
         from itertools import product
         import multiprocessing
-        names = ['Brown', 'Wilson', 'Bartlett', 'Rivera', 'Molloy', 'Opie']
+
+        names = ["Brown", "Wilson", "Bartlett", "Rivera", "Molloy", "Opie"]
         with multiprocessing.Pool(processes=3) as pool:
             results = pool.starmap(self.merge_names, product(names, repeat=2))
         assert results is not None
diff --git a/tests/test_data/IniFile/fm2prof.ini b/tests/test_data/IniFile/fm2prof.ini
new file mode 100644
index 00000000..509ac837
--- /dev/null
+++ b/tests/test_data/IniFile/fm2prof.ini
@@ -0,0 +1,22 @@
+[InputFiles]
+FM_netCDFile				= tests/external_test_data/case_08_waal/Data/FM/FlowFM_fm2prof_map.nc	# Output file from FM2D model (.net file)
+CrossSectionLocationFile	= tests/external_test_data/case_08_waal/Data/cross_section_locations.xyz	# .csv or .txt file that contains four columns: X_coordinate,Y_coordinate,CrossSectionName,Length.
+RegionPolygonFile			= tests/external_test_data/AreaPolygons/Simple	# User defined polygons in json format in the directory; all json files in this directory are used; if not specified, FM2PROF uses the default
+SectionPolygonFile			= 	# Fraction of section 1-4 in each polygon
+
+[InputParameters]
+number_of_css_points	=	20	# INT Number of points which are used to generate cross-sections (default = 20)
+transitionheight_sd	=	0.25		# FLOAT Transition height at the summer dike (m) (default = 0.5)
+velocity_threshold	=	0.01	# FLOAT Absolute velocity threshold in m/s
+relative_threshold	=	0.03	# FLOAT Relative velocity threshold (percent of mean flow velocity; 0-1)
+min_depth_storage	=	0.02	# FLOAT Minimum depth (m) for storage identification (default = 0.02)
+plassen_timesteps	=	10		# INT Number of timesteps that are used for identifying lakes (default=10)
+storagemethod_wli	=	1		# INT Add storage to water level independent cross-section section (1 or 0)
+bedlevelcriterium	=	0.1		# FLOAT Ignore the lowest percentage of bed level points (?)
+SDstorage			=	1		# INT Summer dike option on/off (1 or 0)
+Frictionweighing	=	0		# INT Weighted average for roughness calculation (1) or the orginary arithmetric mean (0)
+sectionsmethod		=	1		# INT Define cross-section sections with user-defined polygon (description)
+
+[OutputDirectory]
+OutputDir = tmp					# DIR Output files are saved in OutputDir/CaseName; if not specified, subdirectory is created in the current directory
+CaseName = 						# STR Subdirectory name under OutputDir (no space); if not specified, "CaseXX" (01, 02..) are used
\ No newline at end of file
diff --git a/tests/test_data/IniFile/invalid_ini_file.ini b/tests/test_data/IniFile/invalid_ini_file.ini
new file mode 100644
index 00000000..d14aec77
--- /dev/null
+++ b/tests/test_data/IniFile/invalid_ini_file.ini
@@ -0,0 +1,8 @@
+FM_netCDFile				= 
+CrossSectionLocationFile	
+gebiedsvakken_dir			=	# User defined polygon; if not specified, FM2PROF uses the default
+SectionFractionFile			= 	# Fraction of section 1-4 in each polygon
+
+[InputParameters]
+number_of_css_points	=	20	# INT Number of points which are used to generate cross-sections (default = 20)
+transitionheight_sd	=	0.25		# FLOAT Transition height at the summer dike (m) (default = 0.5)
\ No newline at end of file
diff --git a/tests/test_data/IniFile/valid_dummy_inifile.ini b/tests/test_data/IniFile/valid_dummy_inifile.ini
new file mode 100644
index 00000000..658c904d
--- /dev/null
+++ b/tests/test_data/IniFile/valid_dummy_inifile.ini
@@ -0,0 +1,10 @@
+[section_zero]
+Option_ZERO_Zero = string	 # Output file from FM2D model (.net file)
+Option_Zero_One	 = 4.2 # .csv or .txt file that contains four columns: X_coordinate,Y_coordinate,CrossSectionName,Length.
+
+[section_one]
+Option_One_Zero =	42	# INT Number of points which are used to generate cross-sections (default = 20)
+Option_One_Two = string
+
+[section_two]
+# no options
\ No newline at end of file
diff --git a/tests/test_data/IniFile/valid_ini_file.ini b/tests/test_data/IniFile/valid_ini_file.ini
new file mode 100644
index 00000000..d242a9d9
--- /dev/null
+++ b/tests/test_data/IniFile/valid_ini_file.ini
@@ -0,0 +1,28 @@
+[input]
+2DMapOutput                   = dummy.nc# Output file from FM2D model (.net file)
+CrossSectionLocationFile      = dummy.xyz# .csv or .txt file (, as delimiter) that contains four columns: X_coordinate,Y_coordinate,BranchName,Length,Chainage.
+RegionPolygonFile             =           # User defined polygons in json format
+SectionPolygonFile            =           # User defined polygons in json format
+
+[parameters]
+CaseName                      =           # Subdirectory name under OutputDir (no space); if not specified, 'CaseXX' (01, 02..) are used
+MaximumPointsInProfile        = 20        # Number of points which are used to generate cross-sections (value = 20)
+AbsoluteVelocityThreshold     = 0.05      # Absolute velocity threshold in m/s. Used to determine storage
+RelativeVelocityThreshold     = 0.03      # Relative velocity threshold (percent of mean flow velocity; 0-1). Used to determine storage
+MinimumDepthThreshold         = 0.02      # Minimum depth (m) for storage identification
+BedlevelCriterium             = 0.05      # Ignore the lowest percentage of bed level points
+LakeTimesteps                 = 10        # Number of timesteps that are used for identifying lakes (value=10)
+ExtrapolateStorage            = True      # Add storage to water level independent cross-section section
+SDCorrection                  = True      # Use summerdike volume correction
+SDFloodplainBase              = 0.5       # minimum distance between floodplain base level and crest level in meters
+SDTransitionHeight            = 0.5       # Transition height at the summer dike (m)
+SDOptimisationMethod          = 0         # [0] Optimise on Total volume, [1] optimise  on flow volume, [2] optimise on both
+FrictionWeighingMethod        = 0         # Options. [0] arithmetric mean, [1] Weighted average
+ExportMapFiles                = False     # Export detailed map output. Only use for small models or limited number of cross-sections b/c output can be huge.
+CssSelection                  =           # provide comma separated list of ints; e.g. 38, 39, 40. Leave empty to generate all cross-sections
+SkipMaps                      = 1         # number of timesteps to skip at begin of 2D output. Use to skip problems related to initial conditions. 
+ClassificationMethod          = 0         # How to classify 2D output using Section and Region polygons. Options: [0] Do not classify regions or sections. [1] Use DeltaShell
+MinimumTotalWidth             = 0.5       # Minimum width in meters. Zero width may lead to numerical instability in 1D solvers
+
+[output]
+OutputDirectory               = dummy# Output files are saved in OutputDir/CaseName; if not specified, subdirectory is created in the current directory
diff --git a/tests/test_data/Output/WriteMaskOutputFile/mask_points.geojson b/tests/test_data/Output/WriteMaskOutputFile/mask_points.geojson
new file mode 100644
index 00000000..eacfeca0
--- /dev/null
+++ b/tests/test_data/Output/WriteMaskOutputFile/mask_points.geojson
@@ -0,0 +1,27 @@
+{
+    "type": "FeatureCollection",
+    "features": [
+        {
+            "type": "Feature",
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    -11.216111,
+                    28.261124
+                ]
+            },
+            "properties": {}
+        },
+        {
+            "type": "Feature",
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    -160.363901,
+                    83.620762
+                ]
+            },
+            "properties": {}
+        }
+    ]
+}
\ No newline at end of file
diff --git a/tests/test_data/Output/WriteMaskOutputFile/no_mask_points.geojson b/tests/test_data/Output/WriteMaskOutputFile/no_mask_points.geojson
new file mode 100644
index 00000000..f9f334a4
--- /dev/null
+++ b/tests/test_data/Output/WriteMaskOutputFile/no_mask_points.geojson
@@ -0,0 +1,4 @@
+{
+    "type": "FeatureCollection",
+    "features": null
+}
\ No newline at end of file
diff --git a/tests/test_data/functions_test_data/cross_section_locations.xyz b/tests/test_data/functions_test_data/cross_section_locations.xyz
new file mode 100644
index 00000000..5a6cb460
--- /dev/null
+++ b/tests/test_data/functions_test_data/cross_section_locations.xyz
@@ -0,0 +1,2 @@
+25,75,case1,250,0
+475,75,case1,500,500
diff --git a/tests/test_data/maskoutputfile_test_data/mask_points.geojson b/tests/test_data/maskoutputfile_test_data/mask_points.geojson
new file mode 100644
index 00000000..32b8f7ff
--- /dev/null
+++ b/tests/test_data/maskoutputfile_test_data/mask_points.geojson
@@ -0,0 +1 @@
+{"type": "FeatureCollection", "features": [{"type": "Feature", "geometry": {"type": "Point", "properties": {}, "coordinates": [4.2, 4.2]}, "properties": {}}, {"type": "Feature", "geometry": {"type": "Point", "properties": {}, "coordinates": [42, 42]}, "properties": {}}]}
\ No newline at end of file
diff --git a/tests/test_data/maskoutputfile_test_data/no_content.geojson b/tests/test_data/maskoutputfile_test_data/no_content.geojson
new file mode 100644
index 00000000..e69de29b
diff --git a/tests/test_data/maskoutputfile_test_data/no_mask_points.geojson b/tests/test_data/maskoutputfile_test_data/no_mask_points.geojson
new file mode 100644
index 00000000..2b6efbb3
--- /dev/null
+++ b/tests/test_data/maskoutputfile_test_data/no_mask_points.geojson
@@ -0,0 +1 @@
+{"type": "FeatureCollection", "features": null}
\ No newline at end of file
diff --git a/tests/test_data/maskoutputfile_test_data/test_file.wrongextension b/tests/test_data/maskoutputfile_test_data/test_file.wrongextension
new file mode 100644
index 00000000..32b8f7ff
--- /dev/null
+++ b/tests/test_data/maskoutputfile_test_data/test_file.wrongextension
@@ -0,0 +1 @@
+{"type": "FeatureCollection", "features": [{"type": "Feature", "geometry": {"type": "Point", "properties": {}, "coordinates": [4.2, 4.2]}, "properties": {}}, {"type": "Feature", "geometry": {"type": "Point", "properties": {}, "coordinates": [42, 42]}, "properties": {}}]}
\ No newline at end of file
diff --git a/tests/test_maskoutputfile.py b/tests/test_maskoutputfile.py
index 9e21696a..6d85482a 100644
--- a/tests/test_maskoutputfile.py
+++ b/tests/test_maskoutputfile.py
@@ -7,22 +7,20 @@
 import shutil
 import json
 import geojson
-
+from pathlib import Path
 
 from fm2prof.MaskOutputFile import MaskOutputFile
 from tests.TestUtils import TestUtils
 
 
 class MaskOutputFileHelper:
-
     @staticmethod
     def get_mask_point():
-        mask_point = geojson.utils.generate_random('Point')
+        mask_point = geojson.utils.generate_random("Point")
         return mask_point
 
 
 class Test_create_mask_point:
-
     @pytest.mark.unittest
     def test_when_no_coords_does_not_raise(self):
         # 1. Set up test model
@@ -35,15 +33,12 @@ def test_when_no_coords_does_not_raise(self):
         try:
             mask_point = MaskOutputFile.create_mask_point(coords, properties)
         except:
-            pytest.fail('Exception risen but not expected.')
+            pytest.fail("Exception risen but not expected.")
         # 4. Verify final expectations
-        assert mask_point is not None, '' + \
-            'No mask_point generated'
+        assert mask_point is not None, "" + "No mask_point generated"
 
     @pytest.mark.unittest
-    @pytest.mark.parametrize(
-        "coords_values",
-        [(4.2, 2.4), (4.2, 2.4, 42)])
+    @pytest.mark.parametrize("coords_values", [(4.2, 2.4), (4.2, 2.4, 42)])
     def test_when_valid_coords_does_not_raise(self, coords_values: tuple):
         # 1. Set up test model
         coords = coords_values
@@ -54,15 +49,12 @@ def test_when_valid_coords_does_not_raise(self, coords_values: tuple):
         try:
             mask_point = MaskOutputFile.create_mask_point(coords, properties)
         except:
-            pytest.fail('Exception risen but not expected.')
+            pytest.fail("Exception risen but not expected.")
         # 3. Verify final expectations
-        assert mask_point is not None, '' + \
-            'No mask_point generated'
+        assert mask_point is not None, "" + "No mask_point generated"
 
     @pytest.mark.unittest
-    @pytest.mark.parametrize(
-        "coords_values",
-        [(4.2)])
+    @pytest.mark.parametrize("coords_values", [(4.2)])
     def test_when_invalid_coords_raises(self, coords_values: tuple):
         # 1. Set up test model
         coords = coords_values
@@ -76,10 +68,8 @@ def test_when_invalid_coords_raises(self, coords_values: tuple):
             exception_thrown = True
 
         # 3. Verify final expectations
-        assert exception_thrown, '' + \
-            'No exception was thrown but it was expected.'
-        assert mask_point is None, '' + \
-            'Mask point generated but was not expected.'
+        assert exception_thrown, "" + "No exception was thrown but it was expected."
+        assert mask_point is None, "" + "Mask point generated but was not expected."
 
     @pytest.mark.unittest
     def test_when_no_properties_does_not_raise(self):
@@ -93,32 +83,29 @@ def test_when_no_properties_does_not_raise(self):
         try:
             mask_point = MaskOutputFile.create_mask_point(coords, properties)
         except:
-            pytest.fail('Exception risen but not expected.')
+            pytest.fail("Exception risen but not expected.")
         # 4. Verify final expectations
-        assert mask_point is not None, '' + \
-            'No mask_point generated'
+        assert mask_point is not None, "" + "No mask_point generated"
 
 
 class Test_validate_extension:
-
     @pytest.mark.unittest
-    @pytest.mark.parametrize(
-        "file_name",
-        [(None), ('')])
+    @pytest.mark.parametrize("file_name", [(None), ("")])
     def test_when_no_file_path_doesnot_raise(self, file_name):
         try:
             MaskOutputFile.validate_extension(file_name)
         except:
-            pytest.fail('Exception risen but not expected.')
+            pytest.fail("Exception risen but not expected.")
 
     @pytest.mark.unittest
     def test_when_invalid_extension_raises_expected_exception(self):
         # 1. Set up test data
-        file_name = 'test_file.wrongextension'
+        file_name = "test_file.wrongextension"
 
         # 2. Set expectations
-        expected_error = '' + \
-            'Invalid file path extension, should be .json or .geojson.'
+        expected_error = (
+            "" + "Invalid file path extension, should be .json or .geojson."
+        )
 
         # 3. Run test
         with pytest.raises(IOError) as e_info:
@@ -126,33 +113,28 @@ def test_when_invalid_extension_raises_expected_exception(self):
 
         # 4. Verify final expectations
         error_message = str(e_info.value)
-        assert error_message == expected_error, '' + \
-            'Expected exception message {},'.format(expected_error) + \
-            'retrieved {}'.format(error_message)
+        assert error_message == expected_error, (
+            ""
+            + "Expected exception message {},".format(expected_error)
+            + "retrieved {}".format(error_message)
+        )
 
     @pytest.mark.unittest
-    @pytest.mark.parametrize(
-        "file_name",
-        [('n.json'), ('n.geojson')])
+    @pytest.mark.parametrize("file_name", [("n.json"), ("n.geojson")])
     def test_when_valid_extension_does_not_raise(self, file_name):
         try:
             MaskOutputFile.validate_extension(file_name)
         except:
-            pytest.fail('Exception risen but not expected.')
+            pytest.fail("Exception risen but not expected.")
 
 
 class Test_read_mask_output_file:
-
     @pytest.mark.unittest
     @pytest.mark.parametrize(
         "file_path_name",
-        [
-            (None),
-            ('invalidfile.geojson'),
-            ('invalidfile.json'),
-            ('invalidfile.xyz')])
-    def test_when_invalid_file_path_given_then_emtpy_geojson(
-            self, file_path_name):
+        [(None), ("invalidfile.geojson"), ("invalidfile.json"), ("invalidfile.xyz")],
+    )
+    def test_when_invalid_file_path_given_then_emtpy_geojson(self, file_path_name):
         # 1. Set up test data
         read_geojson = None
 
@@ -163,103 +145,92 @@ def test_when_invalid_file_path_given_then_emtpy_geojson(
         try:
             read_geojson = MaskOutputFile.read_mask_output_file(file_path_name)
         except:
-            pytest.fail('Exception thrown but not expected.')
+            pytest.fail("Exception thrown but not expected.")
 
         # 4. Verify final expectations
-        assert read_geojson, '' + \
-            'No geojson data was generated.'
-        assert read_geojson == expected_geojson, '' + \
-            'Expected {} but got {}'.format(expected_geojson, read_geojson)
+        assert read_geojson, "" + "No geojson data was generated."
+        assert read_geojson == expected_geojson, "" + "Expected {} but got {}".format(
+            expected_geojson, read_geojson
+        )
 
     @pytest.mark.integrationtest
     def test_when_file_path_wrong_extension_then_raise_exception(self):
         # 1. Set up test data
-        test_dir = TestUtils.get_local_test_data_dir(
-            'maskoutputfile_test_data')
-        file_name = 'test_file.wrongextension'
-        file_path = os.path.join(test_dir, file_name)
+        file_path = (
+            TestUtils.get_local_test_data_dir("maskoutputfile_test_data")
+            / "test_file.wrongextension"
+        )
         read_geojson_data = None
 
         # 2. Set expectations
-        assert os.path.exists(file_path), '' + \
-            'File {} could not be found.'.format(file_path)
-        expected_error = '' + \
-            'Invalid file path extension, should be .json or .geojson.'
+        assert file_path.exists(), "" + "File {} could not be found.".format(file_path)
+        expected_error = (
+            "" + "Invalid file path extension, should be .json or .geojson."
+        )
 
         # 3. Run test
         with pytest.raises(IOError) as e_info:
-            read_geojson_data = MaskOutputFile.read_mask_output_file(file_path)
+            read_geojson_data = MaskOutputFile.read_mask_output_file(str(file_path))
 
         # 4. Verify final expectations
         assert not read_geojson_data
         error_message = str(e_info.value)
-        assert error_message == expected_error, '' + \
-            'Expected exception message {},'.format(expected_error) + \
-            'retrieved {}'.format(error_message)
+        assert error_message == expected_error, (
+            ""
+            + "Expected exception message {},".format(expected_error)
+            + "retrieved {}".format(error_message)
+        )
 
     @pytest.mark.systemtest
     @pytest.mark.parametrize(
-        "file_name",
-        [('no_mask_points.geojson'), ('no_content.geojson')])
+        "file_name", [("no_mask_points.geojson"), ("no_content.geojson")]
+    )
     def test_when_valid_file_with_no_content_then_returns_expected_geojson(
-            self, file_name):
+        self, file_name
+    ):
         # 1. Set up test data
-        test_dir = TestUtils.get_local_test_data_dir(
-            'maskoutputfile_test_data')
-        file_path = os.path.join(test_dir, file_name)
+        file_path: Path = (
+            TestUtils.get_local_test_data_dir("maskoutputfile_test_data") / file_name
+        )
 
-        # 2. Set up initial expectations
         expected_geojson = geojson.FeatureCollection(None)
-        assert os.path.exists(file_path), '' + \
-            'File not found at {}'.format(file_path)
+        assert file_path.is_file(), "File not found at {}".format(file_path)
 
         # 2. Read data
-        try:
-            read_geojson = MaskOutputFile.read_mask_output_file(file_path)
-        except:
-            pytest.fail('Exception thrown but not expected.')
+        read_geojson = MaskOutputFile.read_mask_output_file(str(file_path))
 
         # 3. Verify final expectations
-        assert read_geojson, '' + \
-            'No geojson data was generated.'
-        assert read_geojson == expected_geojson, '' + \
-            'Expected {} but got {}'.format(expected_geojson, read_geojson)
+        assert read_geojson, "No geojson data was generated."
+        assert (
+            read_geojson == expected_geojson
+        ), f"Expected {expected_geojson} but got {read_geojson}"
 
     @pytest.mark.systemtest
-    def test_when_valid_file_with_content_then_returns_expected_geojson(
-            self):
+    def test_when_valid_file_with_content_then_returns_expected_geojson(self):
         # 1. Set up test data
-        test_dir = TestUtils.get_local_test_data_dir(
-            'maskoutputfile_test_data')
-        file_name = 'mask_points.geojson'
-        file_path = os.path.join(test_dir, file_name)
+        file_path = (
+            TestUtils.get_local_test_data_dir("maskoutputfile_test_data")
+            / "mask_points.geojson"
+        )
 
         # 2. Verify initial expectations
-        assert os.path.exists(file_path), '' + \
-            'File not found at {}'.format(file_path)
+        assert file_path.exists(), f"File not found at {file_path}"
 
         # 2. Read data
-        try:
-            read_geojson = MaskOutputFile.read_mask_output_file(file_path)
-        except:
-            pytest.fail('Exception thrown but not expected.')
+        read_geojson = MaskOutputFile.read_mask_output_file(str(file_path))
 
         # 3. Verify final expectations
-        assert read_geojson, '' + \
-            'No geojson data was generated.'
-        assert read_geojson.is_valid, '' + \
-            'The geojson data is not valid.'
+        assert read_geojson, "" + "No geojson data was generated."
+        assert read_geojson.is_valid, "" + "The geojson data is not valid."
 
 
 class Test_write_mask_output_file:
-
-    @pytest.fixture(scope='class')
+    @pytest.fixture(scope="class")
     def test_folder(self):
-        """Prepares the class properties to be used in the tests.
-        """
-        test_dir = TestUtils.get_test_dir('Output\\WriteMaskOutputFile')
-        if not os.path.exists(test_dir):
-            os.makedirs(test_dir)
+        """Prepares the class properties to be used in the tests."""
+        test_dir = TestUtils.get_local_test_data_dir("Output") / "WriteMaskOutputFile"
+        if not test_dir.is_dir():
+            test_dir.mkdir(parents=True, exist_ok=True)
         yield test_dir
 
     @pytest.mark.unittest
@@ -271,17 +242,18 @@ def test_when_no_file_path_given_then_exception_not_risen(self):
         try:
             MaskOutputFile.write_mask_output_file(file_path, mask_points)
         except:
-            pytest.fail('Exception thrown but not expected.')
+            pytest.fail("Exception thrown but not expected.")
 
     @pytest.mark.integrationtest
     def test_when_file_path_with_wrong_extension_then_exception_is_risen(self):
         # 1. Set up test data
-        file_path = 'test_file.wrongextension'
+        file_path = "test_file.wrongextension"
         mask_points = None
 
         # 2. Set expectations
-        expected_error = '' + \
-            'Invalid file path extension, should be .json or .geojson.'
+        expected_error = (
+            "" + "Invalid file path extension, should be .json or .geojson."
+        )
 
         # 3. Run test
         with pytest.raises(IOError) as e_info:
@@ -289,15 +261,18 @@ def test_when_file_path_with_wrong_extension_then_exception_is_risen(self):
 
         # 4. Verify final expectations
         error_message = str(e_info.value)
-        assert error_message == expected_error, '' + \
-            'Expected exception message {},'.format(expected_error) + \
-            'retrieved {}'.format(error_message)
+        assert error_message == expected_error, (
+            ""
+            + "Expected exception message {},".format(expected_error)
+            + "retrieved {}".format(error_message)
+        )
 
     @pytest.mark.systemtest
     def test_when_valid_file_path_and_no_mask_point_then_writes_expectations(
-            self, test_folder):
+        self, test_folder
+    ):
         # 1. Set up test data
-        file_name = 'no_mask_points.geojson'
+        file_name = "no_mask_points.geojson"
         file_path = os.path.join(test_folder, file_name)
         mask_points = None
 
@@ -309,32 +284,33 @@ def test_when_valid_file_path_and_no_mask_point_then_writes_expectations(
         try:
             MaskOutputFile.write_mask_output_file(file_path, mask_points)
         except:
-            pytest.fail('Exception thrown but not expected.')
+            pytest.fail("Exception thrown but not expected.")
 
         # 4. Verify final expectations
-        assert os.path.exists(file_path), '' + \
-            'File {} not found.'.format(file_path)
+        assert os.path.exists(file_path), "" + "File {} not found.".format(file_path)
 
         with open(file_path) as geojson_file:
             read_mask_points = geojson.load(geojson_file)
 
-        assert read_mask_points, '' + \
-            'No mask points were read from {}'.format(file_path)
-        assert expected_mask_points == read_mask_points, '' + \
-            'Expected {} ,'.format(expected_mask_points) + \
-            'but got {}'.format(read_mask_points)
+        assert read_mask_points, "" + "No mask points were read from {}".format(
+            file_path
+        )
+        assert expected_mask_points == read_mask_points, (
+            ""
+            + "Expected {} ,".format(expected_mask_points)
+            + "but got {}".format(read_mask_points)
+        )
 
     @pytest.mark.systemtest
     def test_when_valid_file_path_and_mask_points_then_writes_expectations(
-            self, test_folder):
+        self, test_folder
+    ):
         # 1. Set up test data
-        file_name = 'mask_points.geojson'
+        file_name = "mask_points.geojson"
         file_path = os.path.join(test_folder, file_name)
         mask_points = [
-            geojson.Feature(
-                geometry=MaskOutputFileHelper.get_mask_point()),
-            geojson.Feature(
-                geometry=MaskOutputFileHelper.get_mask_point())
+            geojson.Feature(geometry=MaskOutputFileHelper.get_mask_point()),
+            geojson.Feature(geometry=MaskOutputFileHelper.get_mask_point()),
         ]
 
         # 2. Set expectations
@@ -345,17 +321,19 @@ def test_when_valid_file_path_and_mask_points_then_writes_expectations(
         try:
             MaskOutputFile.write_mask_output_file(file_path, mask_points)
         except:
-            pytest.fail('Exception thrown but not expected.')
+            pytest.fail("Exception thrown but not expected.")
 
         # 4. Verify final expectations
-        assert os.path.exists(file_path), '' + \
-            'File {} not found.'.format(file_path)
+        assert os.path.exists(file_path), "" + "File {} not found.".format(file_path)
 
         with open(file_path) as geojson_file:
             read_mask_points = geojson.load(geojson_file)
 
-        assert read_mask_points, '' + \
-            'No mask points were read from {}'.format(file_path)
-        assert expected_mask_points == read_mask_points, '' + \
-            'Expected {} ,'.format(expected_mask_points) + \
-            'but got {}'.format(read_mask_points)
+        assert read_mask_points, "" + "No mask points were read from {}".format(
+            file_path
+        )
+        assert expected_mask_points == read_mask_points, (
+            ""
+            + "Expected {} ,".format(expected_mask_points)
+            + "but got {}".format(read_mask_points)
+        )