Release 1.1.0 🎉 (#57)

* feat: support Python 3.7+; drop Python 2.7,<3.7 * feat: pass through json serialization options * docs: add advanced usage examples * feat: spec-compliant routes, with legacy support * fix: remove debug messages * test: increase unit test coverage (#52) * test: increase unit test coverage * Update tests.yml --------- Co-authored-by: Liam Beckman <[email protected]> * docs: browsable API reference on GitHub Pages (#49) * docs: browsable API reference on GitHub Pages * Update tests.yml --------- Co-authored-by: Liam Beckman <[email protected]> * Minor release testing updates * Update support for Service Info (#55) - Fix version to match PyPi release (#59) * Add integration test with Funnel * Add initial TES integration test (Funnel) * Add Tmate debug session * Update Funnel installation * Re-add all unit tests * Fix Funnel download issue with correct rc version * Add latest stable Python to test matrix * Fix unit tests not reaching Funnel * Increase test coverage * Minor linting fix * Update raised exception for invalid server response * Update README * Update README.md * Exclude tests from packages (#58) * Add in 3 fields missing in the models for tes. --------- Co-authored-by: Alex Kanitz <[email protected]> Co-authored-by: Kyle Ellrott <[email protected]> Co-authored-by: Ben Beasley <[email protected]> Co-authored-by: Venkat Malladi <[email protected]>
ohsu-comp-bio · Nov 1, 2024 · f2e6909 · f2e6909
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diff --git a/.coverage b/.coverage
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -0,0 +1,36 @@
+name: Building & publishing docs
+
+on:
+  push:
+    branches: [master,api-docs]
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+
+      - name: Install requirements
+        run: pip install -r docs/requirements.txt
+
+      - name: Install app
+        run: pip install .
+
+      - name: Create markdown documents
+        run: |
+          lazydocs \
+              --output-path="./docs/docstrings" \
+              --overview-file="README.md" \
+              --src-base-url="https://github.com/ohsu-comp-bio/py-tes/blob/master/" \
+              --validate \
+              tes
+
+      - name: Build docs
+        run: mkdocs build
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -1,26 +1,47 @@
-name: py-test_file
+name: Linting and testing
 
-on: [ pull_request ]
+on: [pull_request]
 
 jobs:
-
   test:
     runs-on: ubuntu-latest
-    steps:
-    - name: Check out code
-      uses: actions/checkout@v2
-
-    - name: Requirements
-      run: pip install -r requirements.txt
 
-    - name: Test Requirements
-      run: pip install -r tests/requirements.txt
+    strategy:
+      fail-fast: false
+      matrix:
+        version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
 
-    - name: Install
-      run: python setup.py install --user
-
-    - name: Flake
-      run: flake8 .
-
-    - name: Test
-      run: python -m nose tests --with-coverage --cover-package tes --cover-min-percentage 80
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.version }}
+
+      - name: Install requirements
+        run: |
+          pip install -r requirements.txt
+          pip install -r tests/requirements.txt
+
+      - name: Install app
+        run: pip install .
+
+      - name: Lint with Flake8
+        run: flake8 --max-line-length=120 .
+
+      - name: Run unit tests
+        run: |
+          pytest \
+            --cov=tes/ \
+            --cov-branch \
+            --cov-report=term-missing \
+            --cov-fail-under=99 \
+            --ignore=tests/integration
+
+      - name: Run integration tests
+        run: |
+          /bin/bash -c "$(curl -fsSL https://github.com/ohsu-comp-bio/funnel/releases/download/0.11.0-rc.5/install.sh)" -- 0.11.0-rc.5
+          funnel server --LocalStorage.AllowedDirs $HOME run &
+          pytest tests/integration
diff --git a/.gitignore b/.gitignore
@@ -16,5 +16,181 @@ eggs/
 \#*\#
 .desktop
 
+# Misc
 test_tmp
-*venv*
+*venv*
+docs/docstrings
+
+# Created by https://www.toptal.com/developers/gitignore/api/python
+# Edit at https://www.toptal.com/developers/gitignore?templates=python
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+### Python Patch ###
+# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration
+poetry.toml
+
+# ruff
+.ruff_cache/
+
+# End of https://www.toptal.com/developers/gitignore/api/python
diff --git a/.travis.yml b/.travis.yml