Merge with sportran master

.github/CODEOWNERS

@@ -0,0 +1,4 @@
+# The following owners will be the default owners for everything
+# in the repo unless a later match takes precedence.
+sportran/      @lorisercole
+sportran_gui/  @rikigigi

.github/workflows/check_release_tag.py

@@ -0,0 +1,16 @@
+# -*- coding: utf-8 -*-
+"""Check that the GitHub release tag matches the package version."""
+import argparse
+import json
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('GITHUB_REF', help='The GITHUB_REF environmental variable')
+    parser.add_argument('SETUP_PATH', help='Path to the setup.json')
+    args = parser.parse_args()
+    assert args.GITHUB_REF.startswith('refs/tags/v'), f'GITHUB_REF should start with "refs/tags/v": {args.GITHUB_REF}'
+    tag_version = args.GITHUB_REF[11:]
+    with open(args.SETUP_PATH, encoding='utf8') as handle:
+        data = json.load(handle)
+    pypi_version = data['version']
+    assert tag_version == pypi_version, f'The tag version {tag_version} != {pypi_version} specified in `setup.json`'

.github/workflows/ci.yml

@@ -0,0 +1,69 @@
+name: continuous-integration
+
+on: [push, pull_request]
+
+jobs:
+  pre-commit:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+
+    - name: Cache python dependencies
+      id: cache-pip
+      uses: actions/cache@v1
+      with:
+        path: ~/.cache/pip
+        key: pip-pre-commit-${{ hashFiles('**/setup.json') }}
+        restore-keys:
+          pip-pre-commit-
+
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.8'
+
+    - name: Install python dependencies
+      run:
+        pip install -e .[pre-commit,tests]
+
+    - name: Run pre-commit
+      run:
+        pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
+
+  tests:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+
+    - name: Cache python dependencies
+      id: cache-pip
+      uses: actions/cache@v1
+      with:
+        path: ~/.cache/pip
+        key: pip-pre-commit-${{ hashFiles('**/setup.json') }}
+        restore-keys:
+          pip-pre-commit-
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install python dependencies
+      run: |
+        pip install --upgrade setuptools
+        pip install -e .[tests]
+
+    - name: Test with pytest
+      run: |
+        pytest -sv tests

.github/workflows/publish.yml

@@ -0,0 +1,115 @@
+name: release
+
+# Automate deployment to PyPI when creating a release tag vX.Y.Z
+# will only be published to PyPI if the git tag matches the release version
+# and the pre-commit and tests pass
+
+on:
+  push:
+    tags:
+      - "v[0-9]+.[0-9]+.[0-9]+*"
+jobs:
+
+  check-release-tag:
+
+    # Only run this job on the main repository and not on forks
+    if: github.repository == 'sissaschool/sportran'
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.8'
+    - run: python .github/workflows/check_release_tag.py $GITHUB_REF setup.json
+
+  pre-commit:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+
+    - name: Cache python dependencies
+      id: cache-pip
+      uses: actions/cache@v1
+      with:
+        path: ~/.cache/pip
+        key: pip-pre-commit-${{ hashFiles('**/setup.json') }}
+        restore-keys:
+          pip-pre-commit-
+
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.8'
+
+    - name: Install python dependencies
+      run:
+        pip install -e .[pre-commit,tests]
+
+    - name: Run pre-commit
+      run:
+        pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
+
+  tests:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+
+    - name: Cache python dependencies
+      id: cache-pip
+      uses: actions/cache@v1
+      with:
+        path: ~/.cache/pip
+        key: pip-pre-commit-${{ hashFiles('**/setup.json') }}
+        restore-keys:
+          pip-pre-commit-
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install python dependencies
+      run: |
+        pip install --upgrade setuptools
+        pip install -e .[tests]
+
+    - name: Test with pytest
+      run: |
+        pytest -sv tests
+
+  publish:
+
+    name: Publish to PyPI
+
+    needs: [check-release-tag, pre-commit, tests]
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout source
+      uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.8'
+    - name: Build package
+      run: |
+        pip install wheel
+        python setup.py sdist bdist_wheel
+    - name: Publish to PyPI
+      uses: pypa/[email protected]
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_SPORTRAN }}

.gitignore

@@ -24,6 +24,7 @@ wheels/
 *.egg-info/
 .installed.cfg
 *.egg
+metadata.json
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -46,12 +47,14 @@ coverage.xml
 *.cover
 .hypothesis/
 
+# Visual Studio Code
+.vscode/
+
 # Translations
 *.mo
 *.pot
 
 # Django stuff:
-*.log
 local_settings.py
 
 # Flask stuff:

.pre-commit-config.yaml

@@ -1,51 +1,60 @@
 # Install pre-commit hooks via
 # pre-commit install
 
-- repo: local
+repos:
+- repo: https://github.com/pre-commit/mirrors-yapf
+  rev: v0.32.0
   hooks:
-  # yapf = yet another python formatter
   - id: yapf
     name: yapf
-    entry: yapf
-    language: system
     types: [python]
-    args: ["-i"]
+    args: ['-i']
     exclude: &exclude_files >
       (?x)^(
-        thermocepstrum_gui/utils/tk_html_widgets/*.py|
+        sportran/utils/obsolete/.*|
+        sportran_gui/utils/tk_html_widgets/*.py|
         docs/.*|
+        tests/test_cli/.*|
         examples/.*|
         setup.py|
       )$
+    additional_dependencies: ['toml']
 
-- repo: git://github.com/pre-commit/pre-commit-hooks
-  rev: v2.3.0
+- repo: https://github.com/pre-commit/pre-commit-hooks.git
+  rev: v4.1.0
   hooks:
-  - id: check-yaml
+  - id: check-ast
+  - id: check-builtin-literals
+  - id: check-docstring-first
+  - id: check-executables-have-shebangs
+  - id: check-json
   - id: check-merge-conflict
+  - id: check-shebang-scripts-are-executable
   - id: check-symlinks
-  - id: check-json
-  - id: check-executables-have-shebangs
+  - id: check-toml
+  - id: check-yaml
   - id: double-quote-string-fixer
+  - id: fix-encoding-pragma
   - id: end-of-file-fixer
+    exclude: >
+      (?x)^(
+        tests/test_cli/.*|
+        sportran/utils/obsolete/.*|
+      )$
   - id: trailing-whitespace
     exclude: >
       (?x)^(
-        thermocepstrum_gui/utils/tk_html_widgets/*.py|
+        sportran/utils/obsolete/.*|
+        sportran_gui/utils/tk_html_widgets/.*py|
         docs/.*|
+        tests/test_cli/.*|
+        tests/test_notebooks/.*|
         examples/.*|
       )$
-
-#  # prospector: collection of linters
-#  - id: prospector
-#    language: system
-#    types: [file, python]
-#    name: prospector
-#    description: "This hook runs Prospector: https://github.com/landscapeio/prospector"
-#    entry: prospector
 #
-#  - id: version-number
-#    name: Check version numbers
-#    entry: python ./.travis-data/check_version.py
-#    language: system
-#    files: '^(setup.json)|(aiida_diff/__init__.py)'
+#-  repo: https://github.com/PyCQA/pylint
+#   rev: v2.12.2
+#   hooks:
+#   - id: pylint
+#     language: system
+#     exclude: *exclude_files

.readthedocs.yaml

@@ -0,0 +1,32 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+    # You can also specify other tool versions:
+    # nodejs: "16"
+    # rust: "1.55"
+    # golang: "1.17"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/source/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+#    - pdf
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - method: pip
+     path: .
+     extra_requirements:
+       - doc

MANIFEST.in

@@ -1,11 +1,11 @@
 recursive-include examples *
 include LICENSE.txt
 include setup.json
-include thermocepstrum/README.md
-include thermocepstrum/metadata.json
-include thermocepstrum/utils/plot_style.mplstyle
-exclude thermocepstrum/utils/blocks.py
-exclude thermocepstrum/utils/blockanalysis.py
-include thermocepstrum_gui/README_GUI.md
-include thermocepstrum_gui/assets/icon.gif
-include thermocepstrum_gui/assets/languages.json
+include sportran/README.md
+include sportran/metadata.json
+exclude sportran/utils/obsolete/
+include sportran_gui/README_GUI.md
+include sportran_gui/assets/icon.gif
+include sportran_gui/assets/languages.json
+include sportran/plotter/styles/api_style.mplstyle
+include sportran/plotter/styles/cli_style.mplstyle