Merge pull request #215 from saraedum/pixi

Use pixi instead of a conda setup
echemdb · Jan 21, 2025 · c349c43 · c349c43
2 parents ac44d03 + 23d82b2
commit c349c43
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diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -14,34 +14,19 @@ jobs:
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
     steps:
-      - uses: actions/checkout@v2
-        with: { submodules: recursive }
-      - uses: conda-incubator/setup-miniconda@v2
-        with: { miniforge-variant: "Mambaforge" }
-      - name: install dependencies
-        shell: bash -l {0}
-        run: |
-          mamba env update --quiet -n test -f environment.yml
-          conda list
-      - name: install echemdb-website
-        shell: bash -l {0}
-        run: |
-          pip install -e .
+      - uses: actions/checkout@v3
+      - uses: prefix-dev/[email protected]
+        with:
+          pixi-version: v0.39.5
       - name: mkdocs
-        shell: bash -l {0}
-        run: |
+        env:
           # Since no browser is installed during this CI run, plotly fails to
           # produce HTML output, see https://github.com/plotly/plotly.py/blob/2c2dd6ab2eeff73c782457f33c590c1d09a97625/packages/python/plotly/plotly/io/_renderers.py#L532
-          export PLOTLY_RENDERER=browser
-          mkdocs build --strict
-          mv data generated/website/
+          PLOTLY_RENDERER: browser
+        run: |
+          pixi run doc --strict
           # Disable further processing by GitHub
           touch generated/website/.nojekyll
-      - name: fix permissions
-        shell: bash -l {0}
-        run: |
-          # Strangely, the linkchecker modules are installed writable and linkchecker then refuses to load them.
-          chmod -R a-w `python -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())"`
       - name: detect broken links
         shell: bash -l {0}
         run: |
@@ -50,7 +35,7 @@ jobs:
           # We check for broken links:
           # * ignore fonts.gstatic.com which is mentioned by a link preconnect tag that linkchecker does not parse correctly.
           # * ignore DOIs since some publishers ban GitHub or bots.
-          linkchecker --check-extern --no-robots --ignore fonts.gstatic.com --ignore doi.org http://localhost:8880/ --ignore mybinder.org --ignore osti.gov --no-warnings
+          pixi run linkchecker --check-extern --no-robots --ignore fonts.gstatic.com --ignore doi.org http://localhost:8880/ --ignore mybinder.org --ignore osti.gov --no-warnings
         # We only check links on Linux since we do not want to get flagged because of too many requests by the target websites.
         if: ${{ matrix.os == 'ubuntu-latest' }}
       - uses: JamesIves/[email protected]
@@ -60,6 +45,3 @@ jobs:
           target-folder: ""
           single-commit: true
         if: ${{ github.event_name == 'push' && matrix.os == 'ubuntu-latest' }}
-
-env:
-  MAKEFLAGS: -j2
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -9,26 +9,15 @@ concurrency:
 
 jobs:
   python-linter:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
-      - uses: actions/checkout@v2
-        with: { submodules: recursive }
-      - uses: conda-incubator/setup-miniconda@v2
-        with: { miniforge-variant: "Mambaforge" }
-      - name: install dependencies
-        shell: bash -l {0}
-        run: |
-          mamba env update --quiet -n test -f environment.yml
-          conda list
+      - name: checkout
+        uses: actions/checkout@v3
+      - uses: prefix-dev/[email protected]
+        with: { pixi-version: v0.39.5 }
       - name: pylint
-        shell: bash -l {0}
-        run: |
-          pylint website
+        run: pixi run pylint
       - name: black
-        shell: bash -l {0}
-        run: |
-          black --check --diff website
+        run: pixi run black --diff --check
       - name: isort
-        shell: bash -l {0}
-        run: |
-          isort --check --diff --profile black website
+        run: pixi run isort --check --diff
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -13,22 +13,9 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python: ["3.9", "3.10"]
     steps:
-      - uses: actions/checkout@v2
-        with: { submodules: recursive }
-      - uses: conda-incubator/setup-miniconda@v2
-        with: { miniforge-variant: "Mambaforge", python-version: "${{ matrix.python }}" }
-      - name: install dependencies
-        shell: bash -l {0}
-        run: |
-          mamba env update --quiet -n test -f environment.yml
-          conda list
-      - name: install echemdb-website
-        shell: bash -l {0}
-        run: |
-          pip install -e .
-      - name: doctest
-        shell: bash -l {0}
-        run: |
-          pytest -n auto --doctest-plus --doctest-modules website
+      - uses: actions/checkout@v3
+      - uses: prefix-dev/[email protected]
+        with:
+          pixi-version: v0.39.5
+      - run: pixi run doctest
diff --git a/README.md b/README.md
@@ -1,82 +1,35 @@
-The [echemdb repository](https://github.com/echemdb/website) contains high
-quality experimental and theoretical data on electrochemical systems. The
+This project builds a website from the [eletrochemistry-data
+repository](https://github.com/echemdb/electrochemistry-data) which contains
+high quality experimental and theoretical data on electrochemical systems. The
 standardized and validated data displayed on the [projects
-website](https://www.echemdb.org/) so far is from the community and
+website](https://www.echemdb.org/cv) so far is from the community and
 publications aiming at fullfilling the [FAIR
 principles](https://www.go-fair.org/fair-principles/).
 
 The repository can be browsed on [our
 websites](https://www.echemdb.org/) or explored with a [Python
-API](https://github.com/echemdb/echemdb).
+API](https://github.com/echemdb/unitpackage).
 
 # For developers
 
-The build of the website can be tested locally with the following steps.
-
-## Installation
-
-Clone the repository
+Install [pixi](https://pixi.sh) and clone this repository
 
 ```sh
 git clone [email protected]:echemdb/website.git
 ```
 
-Install dependencies (mamba or conda)
+To preview the website run
 
 ```sh
 cd website
-mamba env create --file environment.yaml
-mamba activate echemdb-website
-pip install -e .
-```
-
-## Build website
-
-```sh
-mkdcos serve
-```
-
-The generated HTML files are located in `generated/website`
-
-Entries for the individual cyclic voltammograms are created from datapackaes in `data/generated/svgdigitizer`. Follow the next section to create such data.
-
-## Convert literature to datapackages
-
-To digitize all data
-
-```sh
-cd data
-make
+pixi run preview
 ```
 
-To run the svgdigitizer in parallel on 8 cores, use instead
-
-```sh
-make -j8
-```
-
-We can also only digitize a single data set
-
-```sh
-make generated/svgdigitizer/mello_2018_understanding_J3045/mello_2018_understanding_J3045_p1_f1H_black.csv
-```
-
-To digitize data from a different source directory than
-`literature/` use
-
-```sh
-make SOURCE_DIR=/another/path
-```
-
-## Code changes
-
 If you make changes to the code test the modules with
 
 ```sh
-pytest --doctest-modules website
-pylint website
-isort website
-black website
+pixi run doctest
+pixi run lint
 ```
 
 # License