diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 1285f9a..3ea5dfd 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -14,24 +14,26 @@ jobs: strategy: matrix: os: [ubuntu-latest, macos-latest] - python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] + python-version: ["3.9", "3.10", "3.11", "3.12"] steps: - name: Checkout uses: actions/checkout@v4 - - name: Setup Python ${{ matrix.python-version}} - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} + - name: Install Rye + run: | + curl -sSf https://rye.astral.sh/get | RYE_INSTALL_OPTION="--yes" bash + echo "$HOME/.rye/shims" >> $GITHUB_PATH - - name: Install dependencies - run: pip install -e . pytest pytest-cov ruff + - name: Install Python ${{ matrix.python-version }} & dependencies + run: | + rye pin ${{ matrix.python-version }} + rye sync --update-all --all-features - name: Run ruff lint check - run: ruff check --diff + run: rye run ruff check --diff - name: Run ruff format check - run: ruff format --check --diff + run: rye run ruff format --check --diff - name: Run pytest - run: pytest + run: rye run pytest diff --git a/.github/workflows/publish_mkdocs.yml b/.github/workflows/publish_mkdocs.yml index 8732bb1..2399819 100644 --- a/.github/workflows/publish_mkdocs.yml +++ b/.github/workflows/publish_mkdocs.yml @@ -12,15 +12,13 @@ jobs: - name: Checkout uses: actions/checkout@v4 - - name: Setup Python 3.11 - uses: actions/setup-python@v5 - with: - python-version: "3.11" - - - name: Install MkDocs & Plugins + - name: Install Rye run: | - pip install . - pip install mkdocs mkdocs-material mkdocs-jupyter mkdocstrings[python] black + curl -sSf https://rye.astral.sh/get | RYE_INSTALL_OPTION="--yes" bash + echo "$HOME/.rye/shims" >> $GITHUB_PATH + + - name: Install Python & MkDocs & Plugins + run: rye sync - name: Publish document - run: mkdocs gh-deploy --force + run: rye run mkdocs gh-deploy --force diff --git a/.github/workflows/publish_to_pypi.yml b/.github/workflows/publish_to_pypi.yml index 2bb8587..24e3ab7 100644 --- a/.github/workflows/publish_to_pypi.yml +++ b/.github/workflows/publish_to_pypi.yml @@ -15,18 +15,13 @@ jobs: - name: Checkout uses: actions/checkout@v4 - - name: Setup Python 3.11 - uses: actions/setup-python@v5 - with: - python-version: "3.11" - - - name: Install Poetry + - name: Install Rye run: | - curl -sSL https://install.python-poetry.org | python3 - - echo "$HOME/.local/bin" >> $GITHUB_PATH + curl -sSf https://rye.astral.sh/get | RYE_INSTALL_OPTION="--yes" bash + echo "$HOME/.rye/shims" >> $GITHUB_PATH - name: Build - run: poetry build + run: rye build - name: Publish - run: poetry publish -u $PYPI_USERNAME -p $PYPI_PASSWORD + run: rye publish -u $PYPI_USERNAME --token $PYPI_PASSWORD -y diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index e1d73f7..65d94ea 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -2,7 +2,7 @@ # See https://pre-commit.com/hooks.html for more hooks repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.4.4 + rev: v0.6.4 hooks: - id: ruff name: ruff lint check diff --git a/README.md b/README.md index 3cdb553..d0e33b8 100644 --- a/README.md +++ b/README.md @@ -29,7 +29,7 @@ More detailed documentation is available [here](https://moshi4.github.io/pyCircl ## Installation -`Python 3.8 or later` is required for installation. +`Python 3.9 or later` is required for installation. **Install PyPI package:** diff --git a/docs/index.md b/docs/index.md index 7e3c800..f776880 100644 --- a/docs/index.md +++ b/docs/index.md @@ -20,7 +20,7 @@ pyCirclize was inspired by [circlize](https://github.com/jokergoo/circlize) and ## Installation -`Python 3.8 or later` is required for installation. +`Python 3.9 or later` is required for installation. **Install PyPI package:** diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index b123460..0000000 --- a/poetry.lock +++ /dev/null @@ -1,3068 +0,0 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. - 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Python" -authors = ["moshi4"] +authors = [{ name = "moshi4", email = "" }] license = "MIT" -homepage = "https://moshi4.github.io/pyCirclize/" -repository = "https://github.com/moshi4/pyCirclize/" readme = "README.md" keywords = [ "matplotlib", @@ -19,6 +17,36 @@ classifiers = [ "Topic :: Scientific/Engineering :: Bio-Informatics", "Framework :: Matplotlib", ] +requires-python = ">=3.9" +dependencies = [ + "matplotlib>=3.6.3", + "biopython>=1.80", + "numpy>=1.21", + "pandas>=1.3.5", +] + +[project.urls] +homepage = "https://moshi4.github.io/pyCirclize/" +repository = "https://github.com/moshi4/pyCirclize/" + +[tool.hatch.version] +path = "src/pycirclize/__init__.py" + +[tool.rye] +managed = true +dev-dependencies = [ + "ruff>=0.4.0", + "pre-commit>=3.5.0", + "pytest>=8.0.0", + "pytest-cov>=4.0.0", + "ipykernel>=6.13.0", + # docs + "mkdocs>=1.2", + "mkdocstrings[python]>=0.19.0", + "mkdocs-jupyter>=0.21.0", + "mkdocs-material>=8.2", + "black>=22.3.0", +] [tool.pytest.ini_options] minversion = "6.0" @@ -26,7 +54,7 @@ addopts = "--cov=src --tb=long -vv --cov-report=xml --cov-report=term" testpaths = ["tests"] [tool.ruff] -src = ["src", "tests"] +include = ["src/**.py", "tests/**.py"] line-length = 88 # Lint Rules: https://docs.astral.sh/ruff/rules/ @@ -53,27 +81,6 @@ ignore = [ [tool.ruff.lint.pydocstyle] convention = "numpy" -[tool.poetry.dependencies] -python = "^3.8" -matplotlib = ">=3.5.2" -biopython = ">=1.80" -numpy = ">=1.21.1" -pandas = ">=1.3.5" - -[tool.poetry.group.dev.dependencies] -ruff = ">=0.1.6" -pre-commit = ">=3.5.0" -pytest = ">=7.1.2" -pytest-cov = ">=4.0.0" -ipykernel = ">=6.13.0" - -[tool.poetry.group.docs.dependencies] -mkdocs = ">=1.2" -mkdocstrings = { extras = ["python"], version = ">=0.19.0" } -mkdocs-jupyter = ">=0.21.0" -mkdocs-material = ">=8.2" -black = ">=22.10.0" - [build-system] -requires = ["poetry-core>=1.0.0"] -build-backend = "poetry.core.masonry.api" +requires = ["hatchling"] +build-backend = "hatchling.build" diff --git a/requirements-dev.lock b/requirements-dev.lock new file mode 100644 index 0000000..5deb80e --- /dev/null +++ b/requirements-dev.lock @@ -0,0 +1,314 @@ +# generated by rye +# use `rye lock` or `rye sync` to update this lockfile +# +# last locked with the following flags: +# pre: false +# features: [] +# all-features: false +# with-sources: false +# generate-hashes: false +# universal: false + +-e file:. +asttokens==2.4.1 + # via stack-data +attrs==24.2.0 + # via jsonschema + # via referencing +babel==2.16.0 + # via mkdocs-material +beautifulsoup4==4.12.3 + # via nbconvert +biopython==1.84 + # via pycirclize +black==24.8.0 +bleach==6.1.0 + # via nbconvert +certifi==2024.8.30 + # via requests +cfgv==3.4.0 + # via pre-commit +charset-normalizer==3.3.2 + # via requests +click==8.1.7 + # via black + # via mkdocs + # via mkdocstrings +colorama==0.4.6 + # via griffe + # via mkdocs-material +comm==0.2.2 + # via ipykernel +contourpy==1.3.0 + # via matplotlib +coverage==7.6.1 + # via pytest-cov +cycler==0.12.1 + # via matplotlib +debugpy==1.8.5 + # via ipykernel +decorator==5.1.1 + # via ipython +defusedxml==0.7.1 + # via nbconvert +distlib==0.3.8 + # via virtualenv +exceptiongroup==1.2.2 + # via ipython + # via pytest +executing==2.1.0 + # via stack-data +fastjsonschema==2.20.0 + # via nbformat +filelock==3.16.0 + # via virtualenv +fonttools==4.53.1 + # via matplotlib +ghp-import==2.1.0 + # via mkdocs +griffe==1.3.0 + # via mkdocstrings-python +identify==2.6.0 + # via pre-commit +idna==3.8 + # via requests +importlib-metadata==8.4.0 + # via jupyter-client + # via markdown + # via mkdocs + # via mkdocs-get-deps + # via mkdocstrings + # via nbconvert +importlib-resources==6.4.5 + # via matplotlib +iniconfig==2.0.0 + # via pytest +ipykernel==6.29.5 + # via mkdocs-jupyter +ipython==8.18.1 + # via ipykernel +jedi==0.19.1 + # via ipython +jinja2==3.1.4 + # via mkdocs + # via mkdocs-material + # via mkdocstrings + # via nbconvert +jsonschema==4.23.0 + # via nbformat +jsonschema-specifications==2023.12.1 + # via jsonschema +jupyter-client==8.6.2 + # via ipykernel + # via nbclient +jupyter-core==5.7.2 + # via ipykernel + # via jupyter-client + # via nbclient + # via nbconvert + # via nbformat +jupyterlab-pygments==0.3.0 + # via nbconvert +jupytext==1.16.4 + # via mkdocs-jupyter +kiwisolver==1.4.7 + # via matplotlib +markdown==3.7 + # via mkdocs + # via mkdocs-autorefs + # via mkdocs-material + # via mkdocstrings + # via pymdown-extensions +markdown-it-py==3.0.0 + # via jupytext + # via mdit-py-plugins +markupsafe==2.1.5 + # via jinja2 + # via mkdocs + # via mkdocs-autorefs + # via mkdocstrings + # via nbconvert +matplotlib==3.9.2 + # via pycirclize +matplotlib-inline==0.1.7 + # via ipykernel + # via ipython +mdit-py-plugins==0.4.2 + # via jupytext +mdurl==0.1.2 + # via markdown-it-py +mergedeep==1.3.4 + # via mkdocs + # via mkdocs-get-deps +mistune==3.0.2 + # via nbconvert +mkdocs==1.6.1 + # via mkdocs-autorefs + # via mkdocs-jupyter + # via mkdocs-material + # via mkdocstrings +mkdocs-autorefs==1.2.0 + # via mkdocstrings + # via mkdocstrings-python +mkdocs-get-deps==0.2.0 + # via mkdocs +mkdocs-jupyter==0.25.0 +mkdocs-material==9.5.34 + # via mkdocs-jupyter +mkdocs-material-extensions==1.3.1 + # via mkdocs-material +mkdocstrings==0.26.1 + # via mkdocstrings-python +mkdocstrings-python==1.11.1 + # via mkdocstrings +mypy-extensions==1.0.0 + # via black +nbclient==0.10.0 + # via nbconvert +nbconvert==7.16.4 + # via mkdocs-jupyter +nbformat==5.10.4 + # via jupytext + # via nbclient + # via nbconvert +nest-asyncio==1.6.0 + # via ipykernel +nodeenv==1.9.1 + # via pre-commit +numpy==2.0.2 + # via biopython + # via contourpy + # via matplotlib + # via pandas + # via pycirclize +packaging==24.1 + # via black + # via ipykernel + # via jupytext + # via matplotlib + # via mkdocs + # via nbconvert + # via pytest +paginate==0.5.7 + # via mkdocs-material +pandas==2.2.2 + # via pycirclize +pandocfilters==1.5.1 + # via nbconvert +parso==0.8.4 + # via jedi +pathspec==0.12.1 + # via black + # via mkdocs +pexpect==4.9.0 + # via ipython +pillow==10.4.0 + # via matplotlib +platformdirs==4.3.2 + # via black + # via jupyter-core + # via mkdocs-get-deps + # via mkdocstrings + # via virtualenv +pluggy==1.5.0 + # via pytest +pre-commit==3.8.0 +prompt-toolkit==3.0.47 + # via ipython +psutil==6.0.0 + # via ipykernel +ptyprocess==0.7.0 + # via pexpect +pure-eval==0.2.3 + # via stack-data +pygments==2.18.0 + # via ipython + # via mkdocs-jupyter + # via mkdocs-material + # via nbconvert +pymdown-extensions==10.9 + # via mkdocs-material + # via mkdocstrings +pyparsing==3.1.4 + # via matplotlib +pytest==8.3.3 + # via pytest-cov +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 + # via ghp-import + # via jupyter-client + # via matplotlib + # via pandas +pytz==2024.1 + # via pandas +pyyaml==6.0.2 + # via jupytext + # via mkdocs + # via mkdocs-get-deps + # via pre-commit + # via pymdown-extensions + # via pyyaml-env-tag +pyyaml-env-tag==0.1 + # via mkdocs +pyzmq==26.2.0 + # via ipykernel + # via jupyter-client +referencing==0.35.1 + # via jsonschema + # via jsonschema-specifications +regex==2024.7.24 + # via mkdocs-material +requests==2.32.3 + # via mkdocs-material +rpds-py==0.20.0 + # via jsonschema + # via referencing +ruff==0.6.4 +six==1.16.0 + # via asttokens + # via bleach + # via python-dateutil +soupsieve==2.6 + # via beautifulsoup4 +stack-data==0.6.3 + # via ipython +tinycss2==1.3.0 + # via nbconvert +tomli==2.0.1 + # via black + # via coverage + # via jupytext + # via pytest +tornado==6.4.1 + # via ipykernel + # via jupyter-client +traitlets==5.14.3 + # via comm + # via ipykernel + # via ipython + # via jupyter-client + # via jupyter-core + # via matplotlib-inline + # via nbclient + # via nbconvert + # via nbformat +typing-extensions==4.12.2 + # via black + # via ipython + # via mkdocstrings +tzdata==2024.1 + # via pandas +urllib3==2.2.2 + # via requests +virtualenv==20.26.4 + # via pre-commit +watchdog==5.0.2 + # via mkdocs +wcwidth==0.2.13 + # via prompt-toolkit +webencodings==0.5.1 + # via bleach + # via tinycss2 +zipp==3.20.1 + # via importlib-metadata + # via importlib-resources diff --git a/requirements.lock b/requirements.lock new file mode 100644 index 0000000..52e2afb --- /dev/null +++ b/requirements.lock @@ -0,0 +1,51 @@ +# generated by rye +# use `rye lock` or `rye sync` to update this lockfile +# +# last locked with the following flags: +# pre: false +# features: [] +# all-features: false +# with-sources: false +# generate-hashes: false +# universal: false + +-e file:. +biopython==1.84 + # via pycirclize +contourpy==1.3.0 + # via matplotlib +cycler==0.12.1 + # via matplotlib +fonttools==4.53.1 + # via matplotlib +importlib-resources==6.4.5 + # via matplotlib +kiwisolver==1.4.7 + # via matplotlib +matplotlib==3.9.2 + # via pycirclize +numpy==2.0.2 + # via biopython + # via contourpy + # via matplotlib + # via pandas + # via pycirclize +packaging==24.1 + # via matplotlib +pandas==2.2.2 + # via pycirclize +pillow==10.4.0 + # via matplotlib +pyparsing==3.1.4 + # via matplotlib +python-dateutil==2.9.0.post0 + # via matplotlib + # via pandas +pytz==2024.1 + # via pandas +six==1.16.0 + # via python-dateutil +tzdata==2024.1 + # via pandas +zipp==3.20.1 + # via importlib-resources diff --git a/src/pycirclize/__init__.py b/src/pycirclize/__init__.py index ee8ab00..47fedc3 100644 --- a/src/pycirclize/__init__.py +++ b/src/pycirclize/__init__.py @@ -1,6 +1,6 @@ from pycirclize.circos import Circos -__version__ = "1.6.0" +__version__ = "1.7.0" __all__ = [ "Circos", diff --git a/src/pycirclize/parser/genbank.py b/src/pycirclize/parser/genbank.py index 67b9844..a02afc9 100644 --- a/src/pycirclize/parser/genbank.py +++ b/src/pycirclize/parser/genbank.py @@ -236,10 +236,10 @@ def get_seqid2seq(self) -> dict[str, str]: Returns ------- - seqid2seq : dict[str, int] + seqid2seq : dict[str, str] seqid & genome sequence dict """ - return {str(rec.id): rec.seq for rec in self.records} + return {str(rec.id): str(rec.seq) for rec in self.records} def get_seqid2size(self) -> dict[str, int]: """Get seqid & complete/contig/scaffold genome size dict @@ -278,6 +278,10 @@ def get_seqid2features( for rec in self.records: feature: SeqFeature for feature in rec.features: + # Ignore feature if parsing of location fails + if feature.location is None: + continue + # Filter feature by type & strand strand = feature.location.strand if feature_type is not None and feature.type not in feature_type: continue