From 4699d9296b1d98feb3bae04d4216aefa44066ff5 Mon Sep 17 00:00:00 2001 From: Yuliya Dovzhenko Date: Fri, 23 Jul 2021 18:59:27 -0400 Subject: [PATCH 1/6] adding github actions removing travis --- .github/workflows/tests_and_lint.yml | 45 ++++++++++++++++++++++++++++ .travis.yml | 22 -------------- 2 files changed, 45 insertions(+), 22 deletions(-) create mode 100644 .github/workflows/tests_and_lint.yml delete mode 100644 .travis.yml diff --git a/.github/workflows/tests_and_lint.yml b/.github/workflows/tests_and_lint.yml new file mode 100644 index 0000000..5accc43 --- /dev/null +++ b/.github/workflows/tests_and_lint.yml @@ -0,0 +1,45 @@ +name: Tests and lint + +on: + push: + branches: + - main + tags: + - "v*" + pull_request: + branches: + - "*" +jobs: + lint: + runs-on: ubuntu-latest + strategy: + matrix: + python-version: [3.8] + steps: + - name: Install Python dependencies + run: | + pipenv install --dev --deploy --system + pip install -e . + - name: Run lint checks + run: | + pipenv run ./scripts/lint.sh ${{ matrix.lint-flags }} + tests: + runs-on: ubuntu-latest + strategy: + matrix: + python-version: [3.6, 3.7, 3.8, 3.9] + markers: ["not slow", "slow"] + steps: + - uses: actions/checkout@v2 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v2 + with: + python-version: ${{ matrix.python-version }} + - name: Install Python dependencies + run: | + pipenv install --dev --deploy --system + pip install -e . + - name: Test with pytest + run: | + pytest --cov=bubs bubs/tests -m '${{ matrix.markers }}' + codecov diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 0188a36..0000000 --- a/.travis.yml +++ /dev/null @@ -1,22 +0,0 @@ -language: python -cache: pip -dist: xenial - -install: - - pip install --upgrade pip - - pip install --upgrade setuptools pipenv - - pip install -r dev-requirements.txt - -matrix: - include: - - name: "Lint and static analysis" - python: "3.6" - script: - - ./scripts/copyright_line_check.sh - - ./scripts/lint.sh - - name: "Python 3.6 unit tests" - python: "3.6" - script: - - pytest --cov=bubs bubs -after_success: - - coveralls From d4a4f5981c717f0e5b44f84e1f1d38593ec1167e Mon Sep 17 00:00:00 2001 From: Yuliya Dovzhenko Date: Mon, 26 Jul 2021 13:33:32 -0400 Subject: [PATCH 2/6] comments --- .github/workflows/tests_and_lint.yml | 3 +- .idea/bubs.iml | 14 ++ .idea/libraries/R_User_Library.xml | 6 + .idea/misc.xml | 7 + .idea/modules.xml | 8 ++ .idea/vcs.xml | 6 + .idea/workspace.xml | 204 +++++++++++++++++++++++++++ 7 files changed, 247 insertions(+), 1 deletion(-) create mode 100644 .idea/bubs.iml create mode 100644 .idea/libraries/R_User_Library.xml create mode 100644 .idea/misc.xml create mode 100644 .idea/modules.xml create mode 100644 .idea/vcs.xml create mode 100644 .idea/workspace.xml diff --git a/.github/workflows/tests_and_lint.yml b/.github/workflows/tests_and_lint.yml index 5accc43..58ef398 100644 --- a/.github/workflows/tests_and_lint.yml +++ b/.github/workflows/tests_and_lint.yml @@ -35,8 +35,9 @@ jobs: uses: actions/setup-python@v2 with: python-version: ${{ matrix.python-version }} - - name: Install Python dependencies + - name: Set up Python ${{ matrix.python-version }} run: | + python -m pip install --upgrade pipenv wheel pipenv install --dev --deploy --system pip install -e . - name: Test with pytest diff --git a/.idea/bubs.iml b/.idea/bubs.iml new file mode 100644 index 0000000..1d2bcb9 --- /dev/null +++ b/.idea/bubs.iml @@ -0,0 +1,14 @@ + + + + + + + + + + + + \ No newline at end of file diff --git a/.idea/libraries/R_User_Library.xml b/.idea/libraries/R_User_Library.xml new file mode 100644 index 0000000..71f5ff7 --- /dev/null +++ b/.idea/libraries/R_User_Library.xml @@ -0,0 +1,6 @@ + + + + + + \ No newline at end of file diff --git a/.idea/misc.xml b/.idea/misc.xml new file mode 100644 index 0000000..c42650e --- /dev/null +++ b/.idea/misc.xml @@ -0,0 +1,7 @@ + + + + + + \ No newline at end of file diff --git a/.idea/modules.xml b/.idea/modules.xml new file mode 100644 index 0000000..ff85394 --- /dev/null +++ b/.idea/modules.xml @@ -0,0 +1,8 @@ + + + + + + + + \ No newline at end of file diff --git a/.idea/vcs.xml b/.idea/vcs.xml new file mode 100644 index 0000000..94a25f7 --- /dev/null +++ b/.idea/vcs.xml @@ -0,0 +1,6 @@ + + + + + + \ No newline at end of file diff --git a/.idea/workspace.xml b/.idea/workspace.xml new file mode 100644 index 0000000..913de5d --- /dev/null +++ b/.idea/workspace.xml @@ -0,0 +1,204 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + DEFINITION_ORDER + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - 1627079547327 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file From 9944ae46b140ea6f13263f854b1e4149bf7b57df Mon Sep 17 00:00:00 2001 From: Yuliya Dovzhenko Date: Thu, 29 Jul 2021 15:50:04 -0400 Subject: [PATCH 5/6] cleaning up --- .gitignore | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.gitignore b/.gitignore index 894a44c..4caa324 100644 --- a/.gitignore +++ b/.gitignore @@ -35,6 +35,10 @@ MANIFEST pip-log.txt pip-delete-this-directory.txt +# Pycharm stuff +.idea/ + + # Unit test / coverage reports htmlcov/ .tox/ From d161d2c7a6d963cd00e85b2380bc2c585136b5d0 Mon Sep 17 00:00:00 2001 From: Yuliya Dovzhenko Date: Thu, 29 Jul 2021 15:50:04 -0400 Subject: [PATCH 6/6] cleaning up --- .gitignore | 3 ++ .gitignore~ | 104 +++++++++++++++++++++++++++++++++++++++++++ dev-requirements.txt | 2 +- 3 files changed, 108 insertions(+), 1 deletion(-) create mode 100644 .gitignore~ diff --git a/.gitignore b/.gitignore index 894a44c..2bd30f3 100644 --- a/.gitignore +++ b/.gitignore @@ -35,6 +35,9 @@ MANIFEST pip-log.txt pip-delete-this-directory.txt +# Pycharm stuff +.idea/ + # Unit test / coverage reports htmlcov/ .tox/ diff --git a/.gitignore~ b/.gitignore~ new file mode 100644 index 0000000..894a44c --- /dev/null +++ b/.gitignore~ @@ -0,0 +1,104 @@ +# 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/ +*.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/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +.hypothesis/ +.pytest_cache/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# pyenv +.python-version + +# celery beat schedule file +celerybeat-schedule + +# 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/ diff --git a/dev-requirements.txt b/dev-requirements.txt index 9ae9279..ea86653 100644 --- a/dev-requirements.txt +++ b/dev-requirements.txt @@ -1,5 +1,4 @@ funcy>=1.10 -Keras==2.2.4 numpy>=1.10.0 pylint>=2.4.0,<3 pytest @@ -9,3 +8,4 @@ pydocstyle>=4.0.0,<5 isort>=4.0.0,<5 flake8>=3.0.0,<4 tensorflow>=1.13 +coveralls