Make a package (#1)

- Rewrite everything, improve speed and memory usage, fix some bugs.
- Create a package including documentation and tests (just started, needs work).

.github/workflows/documentation.yml

@@ -0,0 +1,47 @@
+name: documentation
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - published
+
+permissions:
+  contents: write
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 100
+          persist-credentials: false
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies
+        shell: bash -l {0}
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r requirements-dev.txt
+
+      - name: Create docs
+        shell: bash -l {0}
+        run: make html
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v4
+        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs/_build/html/
+          force_orphan: true

.github/workflows/linux.yml

@@ -0,0 +1,142 @@
+name: linux
+
+# Only build PRs, the main branch, and releases.
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - published
+  schedule:
+    - cron: "14 14 20 * *"
+
+# Use bash by default in all jobs
+defaults:
+  run:
+    # Using "-l {0}" is necessary for conda environments to be activated
+    # But this breaks on MacOS if using actions/setup-python:
+    # https://github.com/actions/setup-python/issues/132
+    shell: bash
+
+# Cancel any previous run of the test job.
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+
+    name: basic
+    runs-on: ubuntu-latest
+
+    steps:
+
+      # Checks-out your repository under $GITHUB_WORKSPACE
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          # Need to fetch more than the last commit so that setuptools-scm can
+          # create the correct version string. If the number of commits since
+          # the last release is greater than this, the version still be wrong.
+          # Increase if necessary.
+          fetch-depth: 100
+          # The GitHub token is preserved by default but this job doesn't need
+          # to be able to push to GitHub.
+          persist-credentials: false
+
+      # Need the tags so that setuptools-scm can form a valid version number
+      - name: Fetch git tags
+        run: git fetch origin 'refs/tags/*:refs/tags/*'
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies
+        shell: bash -l {0}
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r requirements-dev.txt
+
+      - name: Flake8
+        shell: bash -l {0}
+        run: flake8 docs/conf.py setup.py resmda/ tests/
+
+      - name: Test with pytest
+        shell: bash -l {0}
+        run: |
+          python -m pip install .
+          pytest --cov=resmda
+
+  deploy:
+    needs: test
+    name: Deploy to PyPI
+    runs-on: ubuntu-latest
+    # Only from the origin repository, not forks; only main and tags.
+    if: github.repository_owner == 'tuda' && (github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/'))
+
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          # Need to fetch more than the last commit so that setuptools-scm can
+          # create the correct version string. If the number of commits since
+          # the last release is greater than this, the version will still be
+          # wrong. Increase if necessary.
+          fetch-depth: 100
+          # The GitHub token is preserved by default but this job doesn't need
+          # to be able to push to GitHub.
+          persist-credentials: false
+
+      # Need the tags so that setuptools-scm can form a valid version number
+      - name: Fetch git tags
+        run: git fetch origin 'refs/tags/*:refs/tags/*'
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install build setuptools-scm
+
+      - name: Build source and wheel distributions
+        if: github.ref == 'refs/heads/main'
+        run: |
+          # Change setuptools-scm local_scheme to "no-local-version" so the
+          # local part of the version isn't included, making the version string
+          # compatible with Test PyPI.
+          sed --in-place 's/"root"/"local_scheme":"no-local-version","root"/g' setup.py
+
+      - name: Build source and wheel distributions
+        run: |
+          # Build source and wheel packages
+          python -m build
+          echo ""
+          echo "Generated files:"
+          ls -lh dist/
+
+      - name: Publish to Test PyPI
+        if: success()
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.TEST_PYPI_PASSWORD }}
+          repository_url: https://test.pypi.org/legacy/
+          # Allow existing releases on test PyPI without errors.
+          # NOT TO BE USED in PyPI!
+          skip_existing: true
+
+      - name: Publish to PyPI
+        # Only for releases
+        if: success() && github.event_name == 'release'
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}

.gitignore

@@ -1,104 +1,22 @@
-# Byte-compiled / optimized / DLL files
+# Directories and file types
 __pycache__/
-*.py[cod]
 
-# C and Fortran extensions
-*.so
-*.dylib
-*.dll
-*.slo
-*.lo
-*.o
-*.obj
-*.mod
-*.smod
-*.lai
-*.la
-*.a
-*.lib
-*.exe
-*.out
-*.app
-
-# Distribution / packaging
-.Python
-env/
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-*.egg-info/
-.installed.cfg
-*.egg
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*,cover
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-
-# Sphinx documentation
+# Sphinx
 docs/_build/
+docs/api/resmda*
+docs/savefig/
+docs/gallery/*
 
-# PyBuilder
-target/
-
-# DotEnv configuration
-.env
-
-# Database
-*.db
-*.rdb
-
-# Pycharm
-.idea
-
-# TeX/LaTeX
-*.aux
-*.bbl
-*.blg
-*.synctex.gz
-*.xwm
-
-# IPython NB Checkpoints
-.ipynb_checkpoints/
-
-# exclude compiled binaries
-bin/
+# Pytest and coverage related
+htmlcov
+.coverage
+.pytest_cache/
 
-# exclude data from source control by default
-/data/external
-/data/interim
-/data/processed
-/data/raw
+# setuptools_scm
+resmda/version.py
 
-# exclude external models from source control
-/src/external/
+# Build related
+.eggs/
+build/
+dist/
+resmda.egg-info/