Gzip reading and compression abstraction (#58)

pylhc · Sep 5, 2023 · ff390c1 · ff390c1
1 parent 5adf26f
commit ff390c1
Show file tree

Hide file tree

Showing 14 changed files with 157 additions and 255 deletions.
diff --git a/.github/workflows/README.md b/.github/workflows/README.md
@@ -1,30 +1,28 @@
 # Continous Integration Workflows
 
-This package implements different workflows for CI.
+This package implements different workflows for CI, based on our organisation's common workflows.
 They are organised as follows.
 
 ### Documentation
 
 The `documentation` workflow triggers on any push to master, builds the documentation and pushes it to the `gh-pages` branch (if the build is successful).
-It runs on `ubuntu-latest` and our lowest supported Python version, `Python 3.7`.
 
 ### Testing Suite
 
 Tests are ensured in the `tests` workflow, which triggers on all pushes.
-It runs on a matrix of all supported operating systems (ubuntu-18.04, ubuntu-20.04, ubuntu-22.04, windows-latest and macos-latest) for all supported Python versions (currently `3.7`, `3.8`, `3.9` and `3.10`).
+It runs on a matrix of all supported operating systems for all supported Python versions.
 
 ### Test Coverage
 
 Test coverage is calculated in the `coverage` wokflow, which triggers on pushes to `master` and any push to a `pull request`.
-It runs on `ubuntu-latest` & the lowest supported Python version (`Python 3.7`), and reports the coverage results of the test suite to `CodeClimate`,
-
+It reports the coverage results of the test suite to `CodeClimate`.
 
 ### Regular Testing
 
 A `cron` workflow triggers every Monday at 3am (UTC time) and runs the full testing suite, on all available operating systems and supported Python versions.
-It also runs on `Python 3.x` so that newly released Python versions that would break tests are automatically detected.
+It also runs on `Python 3.x` so that newly released Python versions that would break tests are automatically included.
 
 ### Publishing
 
-Publishing to `PyPI` is done through the `publish` workflow, which triggers anytime a `release` is made of the Github repository.
-It builds a `wheel`, checks it, and pushes to `PyPI` if checks are successful.
+Publishing to `PyPI` is done through the `publish` workflow, which triggers anytime a `release` is made of the GitHub repository.
+It builds a `wheel`, checks it, and pushes to `PyPI` if checks are successful.
diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
@@ -1,10 +1,6 @@
 # Runs all tests and pushes coverage report to codeclimate
 name: Coverage
 
-defaults:
-  run:
-    shell: bash
-
 on:  # Runs on all push events to master branch and any push related to a pull request
   push:
     branches:
@@ -13,59 +9,7 @@ on:  # Runs on all push events to master branch and any push related to a pull r
 
 jobs:
   coverage:
-    name: ${{ matrix.os }} / ${{ matrix.python-version }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:  # only lowest supported Python on latest ubuntu
-        os: [ubuntu-latest]
-        python-version: [3.7]
-
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: '**/setup.py'
-
-      - name: Get full Python version
-        id: full-python-version
-        run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
-
-      - name: Upgrade pip, setuptools and wheel
-        run: python -m pip install --upgrade pip setuptools wheel
-
-      - name: Install package
-        run: python -m pip install '.[test]'
-
-      - name: Set up env for CodeClimate (push)
-        run: |
-          echo "GIT_BRANCH=${GITHUB_REF/refs\/heads\//}" >> $GITHUB_ENV
-          echo "GIT_COMMIT_SHA=$GITHUB_SHA" >> $GITHUB_ENV
-        if: github.event_name == 'push'
-
-      - name: Set up env for CodeClimate (pull_request)
-        env:
-          PR_HEAD_SHA: ${{ github.event.pull_request.head.sha }}
-        run: |
-          echo "GIT_BRANCH=$GITHUB_HEAD_REF" >> $GITHUB_ENV
-          echo "GIT_COMMIT_SHA=$PR_HEAD_SHA" >> $GITHUB_ENV
-        if: github.event_name == 'pull_request'
-
-      - name: Prepare CodeClimate binary
-        env:
-          CC_TEST_REPORTER_ID: ${{ secrets.CC_TEST_REPORTER_ID }}
-        run: |
-          curl -LSs 'https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64' >./cc-test-reporter;
-          chmod +x ./cc-test-reporter
-          ./cc-test-reporter before-build
-      - name: Run all tests
-        run: python -m pytest --cov-report xml --cov=sdds
-
-      - name: Push Coverage to CodeClimate
-        if: ${{ success() }}  # only if tests were successful
-        env:
-          CC_TEST_REPORTER_ID: ${{ secrets.CC_TEST_REPORTER_ID }}
-        run: ./cc-test-reporter after-build
+      uses: pylhc/.github/.github/workflows/coverage.yml@master
+      with:
+        src-dir: sdds
+      secrets: inherit
diff --git a/.github/workflows/cron.yml b/.github/workflows/cron.yml
@@ -1,43 +1,13 @@
-# Runs all tests on master everyday at 10 am (UTC time)
+# Runs all tests on master on Mondays at 3 am (UTC time)
 name: Cron Testing
 
-defaults:
-  run:
-    shell: bash
 
-on:  # Runs on master branch on Mondays at 3am UTC time
+on: 
   schedule:
     - cron:  '* 3 * * mon'
 
 jobs:
-  tests:
-    name: ${{ matrix.os }} / ${{ matrix.python-version }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [ubuntu-18.04, ubuntu-20.04,, ubuntu-22.04, macos-latest, windows-latest]
-        # Make sure to escape 3.10 with quotes so it doesn't get interpreted as float 3.1 by GA's parser
-        python-version: [3.7, 3.8, 3.9, "3.10", 3.x]  # crons should always run latest python hence 3.x
-
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: '**/setup.py'
-
-      - name: Get full Python version
-        id: full-python-version
-        run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
-
-      - name: Upgrade pip, setuptools and wheel
-        run: python -m pip install --upgrade pip setuptools wheel
-
-      - name: Install package
-        run: python -m pip install '.[test]'
-
-      - name: Run all tests
-        run: python -m pytest
+    tests:
+      uses: pylhc/.github/.github/workflows/cron.yml@master
+      with:
+        extra-dependencies: test
diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
@@ -1,51 +1,14 @@
 # Build documentation
+# The build is uploaded as artifact if the triggering event is a push for a pull request
+# The build is published to github pages if the triggering event is a push to the master branch (PR merge)
 name: Build and upload documentation
 
-defaults:
-  run:
-    shell: bash
-
-on:  # Runs on any push event to master
+on:  # Runs on any push event in a PR or any push event to master
+  pull_request:
   push:
     branches:
       - 'master'
 
 jobs:
   documentation:
-    name: ${{ matrix.os }} / ${{ matrix.python-version }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:  # only lowest supported Python on latest ubuntu
-        os: [ubuntu-latest]
-        python-version: [3.7]
-
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: '**/setup.py'
-
-      - name: Get full Python version
-        id: full-python-version
-        run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
-
-      - name: Upgrade pip, setuptools and wheel
-        run: python -m pip install --upgrade pip setuptools wheel
-
-      - name: Install package
-        run: python -m pip install '.[doc]'
-
-      - name: Build documentation
-        run: python -m sphinx -b html doc ./doc_build -d ./doc_build
-
-      - name: Upload documentation to gh-pages
-        if: ${{ success() }}
-        uses: JamesIves/github-pages-deploy-action@3.7.1
-        with:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          BRANCH: gh-pages
-          FOLDER: doc_build
+        uses: pylhc/.github/.github/workflows/documentation.yml@master
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -1,50 +1,11 @@
 # Publishes to PyPI upon creation of a release
 name: Upload Package to PyPI
 
-defaults:
-  run:
-    shell: bash
-
 on:  # Runs everytime a release is added to the repository
   release:
     types: [created]
 
 jobs:
   deploy:
-    name: ${{ matrix.os }} / ${{ matrix.python-version }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:  # only lowest supported Python on latest ubuntu
-        os: [ubuntu-latest]
-        python-version: [3.7]
-
-
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: '**/setup.py'
-
-      - name: Get full Python version
-        id: full-python-version
-        run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
-
-      - name: Upgrade pip, setuptools, wheel, build and twine
-        run: python -m pip install --upgrade pip setuptools wheel build twine
-
-      - name: Build and check build
-        run: |
-          python -m build
-          twine check dist/*
-
-      - name: Publish
-        if: ${{ success() }}
-        env:
-          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-        run: |
-          twine upload dist/*
+    uses: pylhc/.github/.github/workflows/publish.yml@master
+    secrets: inherit
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -1,42 +1,17 @@
 # Runs all tests 
-name: Tests
+name: All Tests
 
 defaults:
   run:
     shell: bash
 
-on:  [push]  # Runs on all push events to any branch
-
+on:  # Runs on any push event to any branch except master (the coverage workflow takes care of that)
+  push:
+    branches-ignore:
+      - 'master'
 
 jobs:
   tests:
-    name: ${{ matrix.os }} / ${{ matrix.python-version }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [ubuntu-18.04, ubuntu-20.04, ubuntu-22.04, macos-latest, windows-latest]
-        # Make sure to escape 3.10 with quotes so it doesn't get interpreted as float 3.1 by GA's parser
-        python-version: [3.7, 3.8, 3.9, "3.10"]
-
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: '**/setup.py'
-
-      - name: Get full Python version
-        id: full-python-version
-        run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
-
-      - name: Upgrade pip, setuptools and wheel
-        run: python -m pip install --upgrade pip setuptools wheel
-
-      - name: Install package
-        run: python -m pip install '.[test]'
-
-      - name: Run basic tests
-        run: python -m pytest
+    uses: pylhc/.github/.github/workflows/tests.yml@master
+    with:
+      extra-dependencies: test
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # SDDS-Files Changelog
 
+## Version 0.4
+- Added:
+    - Support for reading gzipped compressed file and arbitrary compression formats if the opener abstraction is provided.
+
 ## Version 0.3
 - Added:
     - little endian support.

diff --git a/doc/conf.py b/doc/conf.py
@@ -88,7 +88,7 @@ def about_package(init_posixpath: pathlib.Path) -> dict:
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -113,7 +113,7 @@ def about_package(init_posixpath: pathlib.Path) -> dict:
     'collapse_navigation': False,
     'display_version': True,
     'logo_only': True,
-    'navigation_depth': 2,
+    'navigation_depth': 3,
 }
 
 html_logo = '_static/img/omc_logo.svg'

diff --git a/doc/modules/index.rst b/doc/modules/index.rst
@@ -1,15 +1,18 @@
 SDDS Modules
-**************************
+************
 
 .. automodule:: sdds.classes
     :members:
+    :noindex:
 
 
 .. automodule:: sdds.reader
     :members:
+    :noindex:
 
 
 .. automodule:: sdds.writer
     :members:
+    :noindex:
 
 
diff --git a/sdds/__init__.py b/sdds/__init__.py
@@ -1,12 +1,12 @@
 """Exposes SddsFile, read_sdds and write_sdds directly in sdds namespace."""
-from sdds.writer import write_sdds
-from sdds.reader import read_sdds
 from sdds.classes import SddsFile
+from sdds.reader import read_sdds
+from sdds.writer import write_sdds
 
 __title__ = "sdds"
 __description__ = "SDDS file handling."
 __url__ = "https://github.com/pylhc/sdds"
-__version__ = "0.3.1"
+__version__ = "0.4.0"
 __author__ = "pylhc"
 __author_email__ = "pylhc@github.com"
 __license__ = "MIT"