Explicit migration from Travis to Github actions + deps bump (#152)

* Explicit Travis replacement with github actions

* Resolving config issues and linting

* Who looks at examples, eh?

* Bump version to 1.6.0

.github/workflows/ci-lint.yml

@@ -1,26 +1,13 @@
 name: Linter
 
-on: [push]
+on: [push, pull_request]
 
 jobs:
-  build-n-lint:
+  lint:
     runs-on: ubuntu-latest
-
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: psf/black@stable
+      - uses: isort/isort-action@v1
         with:
-          python-version: "3.8"
-
-      - name: Install test dependencies
-        run: |
-          pip install --upgrade pip
-          pip install --only-binary=numpy,scipy numpy scipy
-          pip install -e .[dev]
-      - name: Run ISort check
-        run: python -m isort --check PyEMD
-      - name: Run PyCodeStyle check
-        run: python -m pycodestyle PyEMD
-      - name: Run Black check
-        run: python -m black --check PyEMD
+          sort-paths: PyEMD

.github/workflows/ci-main-build-test-deploy.yml

@@ -0,0 +1,52 @@
+name: Upload Python Package
+
+on:
+  push:
+    paths:
+      - PyEMD/__init__.py
+    branches:
+      - $default-branch
+
+jobs:
+  build-n-test:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: [3.8, 3.9, 3.10, 3.11, 3.12]
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Running Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install test dependencies
+        run: |
+          pip install --only-binary=numpy,scipy numpy scipy
+          pip install -e .[test]
+      - name: Run tests
+        run: |
+          python -m PyEMD.tests.test_all
+
+  deploy:
+    # Run 'deploy' job only if `PyEMD/__init__.py` is modified
+    if: github.event_name == 'push' && contains(github.event.head_commit.modified, 'PyEMD/__init__.py')
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+      - name: Build package
+        run: python -m build
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+        with:
+          user: __token__
+          password: ${{ secrets.EMD_PYPI_API_TOKEN }}

.github/workflows/ci-pr-test.yml

@@ -0,0 +1,37 @@
+name: Test
+
+on:
+  push:
+    branches-ignore:
+      - $default-branch
+  pull_request:
+    paths:
+      - 'PyEMD/**.py'
+
+jobs:
+
+  build-n-test:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: 
+          - "3.8"
+          - "3.9"
+          - "3.10"
+          - "3.11"
+          - "3.12"
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Running Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install test dependencies
+        run: |
+          pip install --only-binary=numpy,scipy numpy scipy
+          pip install -e .[test]
+      - name: Run tests
+        run: |
+          python -m PyEMD.tests.test_all

Makefile

@@ -1,3 +1,4 @@
+LINT_TARGET_DIRS := PyEMD doc example
 
 test:
 	python -m PyEMD.tests.test_all
@@ -10,8 +11,11 @@ doc:
 	cd doc && make html
 
 format:
-	black PyEMD
+	python -m black $(LINT_TARGET_DIRS)
 
 lint-check:
 	python -m isort --check PyEMD
-	python -m black --check PyEMD
+	python -m black --check $(LINT_TARGET_DIRS)
+
+perf/build:
+	docker build -t pyemd-perf -f perf_test/Dockerfile .

PyEMD/__init__.py

@@ -1,6 +1,6 @@
 import logging
 
-__version__ = "1.5.2"
+__version__ = "1.6.0"
 logger = logging.getLogger("pyemd")
 
 from PyEMD.CEEMDAN import CEEMDAN  # noqa

PyEMD/checks.py

@@ -1,4 +1,5 @@
 """Calculate the statistical Significance of IMFs."""
+
 import logging
 import math
 

PyEMD/tests/test_checks.py

@@ -1,4 +1,5 @@
 """Tests for checks.py."""
+
 import unittest
 
 import numpy as np

README.md

@@ -1,5 +1,4 @@
 [![codecov](https://codecov.io/gh/laszukdawid/PyEMD/branch/master/graph/badge.svg)](https://codecov.io/gh/laszukdawid/PyEMD)
-[![Build Status](https://app.travis-ci.com/laszukdawid/PyEMD.svg?branch=master)](https://app.travis-ci.com/laszukdawid/PyEMD)
 [![DocStatus](https://readthedocs.org/projects/pyemd/badge/?version=latest)](https://pyemd.readthedocs.io/)
 [![Codacy Badge](https://app.codacy.com/project/badge/Grade/f56b6fc3f855476dbaebd3c02ae88f3e)](https://www.codacy.com/gh/laszukdawid/PyEMD/dashboard?utm_source=github.com&utm_medium=referral&utm_content=laszukdawid/PyEMD&utm_campaign=Badge_Grade)
 [![DOI](https://zenodo.org/badge/65324353.svg)](https://zenodo.org/badge/latestdoi/65324353)

doc/conf.py

@@ -65,25 +65,25 @@
 master_doc = "index"
 
 # General information about the project.
-project = u"PyEMD"
-copyright = u"2016-{year}, Dawid Laszuk".format(year=datetime.datetime.now().year)
-author = u"Dawid Laszuk"
+project = "PyEMD"
+copyright = "2016-{year}, Dawid Laszuk".format(year=datetime.datetime.now().year)
+author = "Dawid Laszuk"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = u"0.4.0"
+version = "0.4.0"
 # The full version, including alpha/beta/rc tags.
-release = u"0.4.0"
+release = "0.4.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = 'en'
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -142,15 +142,15 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, "PyEMD.tex", u"PyEMD Documentation", u"Dawid Laszuk", "manual"),
+    (master_doc, "PyEMD.tex", "PyEMD Documentation", "Dawid Laszuk", "manual"),
 ]
 
 
 # -- Options for manual page output ---------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [(master_doc, "PyEMD", u"PyEMD Documentation", [author], 1)]
+man_pages = [(master_doc, "PyEMD", "PyEMD Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output -------------------------------------------
@@ -159,7 +159,7 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, "PyEMD", u"PyEMD Documentation", author, "PyEMD", "One line description of project.", "Miscellaneous"),
+    (master_doc, "PyEMD", "PyEMD Documentation", author, "PyEMD", "One line description of project.", "Miscellaneous"),
 ]
 
 

example/eemd_example.py

@@ -12,7 +12,7 @@
 S += 5 * sin(11, 2.7)
 S += 3 * sin(14, 1.6)
 S += 1 * np.sin(4 * 2 * np.pi * (t - 0.8) ** 2)
-S += t ** 2.1 - t
+S += t**2.1 - t
 
 # Assign EEMD to `eemd` variable
 eemd = EEMD()

example/emd_comparison.py

@@ -6,6 +6,7 @@
 a lot of the same computation within a single execution. For a single script
 with a single EMD execution, it's still much more performant to use normal EMD.
 """
+
 import time
 import numpy as np
 
@@ -17,11 +18,13 @@
 t = get_timeline(len(s), s.dtype)
 n_repeat = 20
 
-print(f"""Comparing EEMD execution on a larger signal with classic and JIT EMDs.
+print(
+    f"""Comparing EEMD execution on a larger signal with classic and JIT EMDs.
 Signal is random (uniform) noise of length: {len(s)}. The test is done by executing
 EEMD with either classic or JIT EMD {n_repeat} times and taking the average. Such
 setup favouries JitEMD which is compiled once and then reused {n_repeat-1} times.
-Compiltion is quite costly.""")
+Compiltion is quite costly."""
+)
 
 time_0 = time.time()
 emd = EMD()