Merge pull request #27 from complextissue/dev

Use ruff, require Python 3.10, improve docstrings, add view source to docs

Author: maltekuehl

.github/FUNDING.yml

@@ -0,0 +1 @@
+github: maltekuehl

.github/ISSUE_TEMPLATE/help.md

@@ -7,6 +7,6 @@ assignees: ''
 ---
 
 Ask for help on how to best use `pytximport`. Prior to submitting your question, please read through the follwoing resources:
-- The `pytximport` documentation available at: [https://pytximport.readthedocs.io](https://pytximport.readthedocs.io)
+- The `pytximport` documentation available at: [https://pytximport.complextissue.com](https://pytximport.complextissue.com)
 - The `tximport` documentation available at: [https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html](https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html)
 - The original `tximport` publication by [Soneson et al.](https://f1000research.com/articles/4-1521).

.github/workflows/ci.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: [3.9.16]
+        python-version: [3.12.6]
 
     steps:
       - uses: actions/checkout@v3
@@ -34,21 +34,18 @@ jobs:
           python -m pip install flit
           python -m flit install --deps production
           python -m pip install biocframe dolomite dolomite-se summarizedexperiment
-          python -m pip install black flake8 flake8-docstrings isort flake8-comprehensions mypy
-          python -m pip install coverage pytest bandit sphinx sphinx-autoapi \
-            myst-parser pybiomart pygments sphinx-autodoc-typehints sphinx-rtd-theme furo sphinx_design \
-            sphinx-copybutton sphinxcontrib-bibtex sphinxcontrib-mermaid nbsphinx pandoc
+          python -m pip install bandit mypy ruff==0.11.2
+          python -m pip install coverage pytest sphinx sphinx-autoapi \
+            myst-parser pygments sphinx-autodoc-typehints sphinx-rtd-theme furo sphinx_design sphinx-copybutton \
+            sphinxcontrib-bibtex sphinxcontrib-mermaid nbsphinx pandoc
           sudo apt-get update
           sudo apt-get install -y pandoc
-      - name: Format with black
+      - name: Lint with ruff
         run: |
-          python -m black .
-      - name: Lint with flake8
+          ruff check --fix --exit-non-zero-on-fix pytximport
+      - name: Format with ruff
         run: |
-          python -m flake8 pytximport
-      - name: Check imports with isort
-        run: |
-          python -m isort --check-only --diff --recursive pytximport
+          ruff format --check pytximport
       - name: Type check with mypy
         run: |
           python -m mypy -p pytximport

.pre-commit-config.yaml

@@ -5,58 +5,47 @@ repos:
     rev: v4.4.0
     hooks:
       - id: check-yaml
-        stages: [commit]
+        stages: [pre-commit]
       - id: check-toml
-        stages: [commit]
+        stages: [pre-commit]
       - id: end-of-file-fixer
-        stages: [commit]
+        stages: [pre-commit]
       - id: trailing-whitespace
-        stages: [commit]
+        stages: [pre-commit]
       - id: requirements-txt-fixer
-        stages: [commit]
+        stages: [pre-commit]
       - id: check-added-large-files
-        stages: [commit]
+        stages: [pre-commit]
         args: ["--maxkb=50000"]
       - id: check-case-conflict
-        stages: [commit]
+        stages: [pre-commit]
       - id: mixed-line-ending
-        stages: [commit]
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+        stages: [pre-commit]
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.11.2
     hooks:
-      - id: isort
-        stages: [commit]
-        args: ["--profile", "black", "--filter-files"]
-  - repo: https://github.com/python/black
-    rev: 23.3.0
-    hooks:
-      - id: black
-        stages: [commit]
-        args: [--line-length=120]
-  - repo: https://github.com/pycqa/flake8
-    rev: 6.0.0
-    hooks:
-      - id: flake8
-        stages: [commit]
+      - id: ruff
+        args: [--select, I, --fix]
+      - id: ruff-format
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.3.0"
+    rev: v1.15.0
     hooks:
       - id: mypy
-        stages: [commit]
+        stages: [pre-commit]
         language: system
         pass_filenames: false
         args: [-p, pytximport]
   - repo: https://github.com/PyCQA/bandit
     rev: 1.7.5
     hooks:
       - id: bandit
-        stages: [commit]
+        stages: [pre-commit]
         args: [--verbose, --ini, .bandit.ini, -ll, --recursive, pytximport]
   # run the unittests
   - repo: local
     hooks:
       - id: unittests
-        stages: [commit]
+        stages: [pre-commit]
         name: unittests
         entry: python -m coverage run -m pytest --maxfail=10
         language: system

.vscode/extensions.json

@@ -1,14 +1,12 @@
 {
     "recommendations": [
+        "charliermarsh.ruff",
         "ms-python.python",
         "ms-python.vscode-pylance",
         "ms-python.vscode-pylance-extra-types",
         "ms-python.python-test-adapter",
         "ms-python.vscode-pylance-pack",
-        "ms-python.isort",
         "njpwerner.autodocstring",
-        "ms-python.black-formatter",
-        "ms-python.flake8",
         "shardulm94.trailing-spaces",
         "ms-vscode.makefile-tools",
     ]

.vscode/settings.json

@@ -1,35 +1,44 @@
 {
-  "editor.rulers": [
-    {
-      "column": 120,
-      "color": "#ddd"
-    }
-  ],
-  "editor.tabSize": 4,
-  "editor.insertSpaces": true,
-  "editor.detectIndentation": false,
-  "editor.formatOnSave": true,
-  "python.languageServer": "Pylance",
-  "python.analysis.typeCheckingMode": "off",
-  "[python]": {
-    "editor.formatOnPaste": false, // not supported by black
-    "editor.formatOnSaveMode": "file",
-    "editor.defaultFormatter": "ms-python.black-formatter"
-  },
-  "python.analysis.extraPaths": ["pytximport", "test", "examples"],
-  "python.analysis.exclude": ["**/.venv/**", "**/__pycache__/**"],
-  "python.defaultInterpreterPath": ".venv/bin/python",
-  "isort.args": ["--profile", "black"],
-  "python.testing.unittestEnabled": false,
-  "python.testing.pytestEnabled": true,
-  "files.insertFinalNewline": true,
-  "esbonio.sphinx.confDir": "${workspaceFolder}/docs/source",
-  "trailing-spaces.trimOnSave": true,
-  "notebook.formatOnSave.enabled": true,
-  "notebook.cellFocusIndicator": "gutter",
-  "notebook.lineNumbers": "on",
-  "files.watcherExclude": {
-    "**/.venv/**": true
-  },
-  "githubPullRequests.ignoredPullRequestBranches": ["main"]
+    "[python]": {
+        "editor.defaultFormatter": "charliermarsh.ruff",
+        "editor.formatOnPaste": false,
+        "editor.formatOnSaveMode": "file"
+    },
+    "editor.detectIndentation": false,
+    "editor.formatOnSave": true,
+    "editor.insertSpaces": true,
+    "editor.rulers": [
+        {
+            "color": "#ddd",
+            "column": 120
+        }
+    ],
+    "editor.tabSize": 4,
+    "esbonio.sphinx.confDir": "${workspaceFolder}/docs/source",
+    "files.insertFinalNewline": true,
+    "files.watcherExclude": {
+        "**/.venv/**": true
+    },
+    "githubPullRequests.ignoredPullRequestBranches": [
+        "main"
+    ],
+    "notebook.cellFocusIndicator": "gutter",
+    "notebook.formatOnSave.enabled": true,
+    "notebook.lineNumbers": "on",
+    "python.analysis.exclude": [
+        "**/.venv/**",
+        "**/__pycache__/**"
+    ],
+    "python.analysis.extraPaths": [
+        "examples",
+        "pytximport",
+        "test"
+    ],
+    "python.analysis.typeCheckingMode": "off",
+    "python.defaultInterpreterPath": ".venv/bin/python",
+    "python.languageServer": "Pylance",
+    "python.testing.pytestEnabled": true,
+    "python.testing.unittestEnabled": false,
+    "ruff.organizeImports": true,
+    "trailing-spaces.trimOnSave": true
 }

CITATION.cff

@@ -29,7 +29,7 @@ identifiers:
     value: 10.1093/bioinformatics/btae700
     description: Bioinformatics manuscript
 repository-code: 'https://github.com/complextissue/pytximport'
-url: 'https://pytximport.readthedocs.io'
+url: 'https://pytximport.complextissue.com'
 abstract: >-
   Transcript quantification tools efficiently map bulk RNA
   sequencing reads to reference transcriptomes. However,

Makefile

@@ -27,9 +27,9 @@ install-dev: install
 # Checks & package upload
 #
 check: install-dev
-	isort pytximport
-	black --check pytximport
-	flake8 pytximport
+	ruff format --check pytximport
+	ruff check pytximport
+	mypy -p pytximport
 	bandit -ll --recursive pytximport
 
 upload: check

README.md

@@ -5,21 +5,21 @@
 [![Version](https://img.shields.io/pypi/v/pytximport)](https://pypi.org/project/pytximport/)
 [![License](https://img.shields.io/pypi/l/pytximport)](https://github.com/complextissue/pytximport)
 ![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/complextissue/pytximport/ci.yml)
-[![Documentation Status](https://readthedocs.org/projects/pytximport/badge/?version=latest)](https://pytximport.readthedocs.io/en/latest/?badge=latest)
+[![Documentation Status](https://readthedocs.org/projects/pytximport/badge/?version=latest)](https://pytximport.complextissue.com/en/latest/?badge=latest)
 [![Codecov](https://codecov.io/gh/complextissue/pytximport/graph/badge.svg?token=M9JEHJVXYI)](https://codecov.io/gh/complextissue/pytximport)
 [![Install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/pytximport/README.html)
 ![Conda Downloads](https://img.shields.io/conda/d/bioconda/pytximport)
 ![Pepy Total Downloads](https://img.shields.io/pepy/dt/pytximport?label=PyPi%7Cdownloads)
 [![Python Version Required](https://img.shields.io/pypi/pyversions/pytximport)](https://pypi.org/project/pytximport/)
-[![Code Style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
 
 `pytximport` is a Python package for efficient (gene-)count estimation from transcript quantification files produced by pseudoalignment/quasi-mapping tools such as `salmon`, `kallisto`, `rsem` and others. `pytximport` is a port of the popular [tximport Bioconductor R package](https://bioconductor.org/packages/release/bioc/html/tximport.html).
 
 ## Manuscript & Documentation
 
 The pytximport manuscript can be accessed at: [https://doi.org/10.1093/bioinformatics/btae700](https://doi.org/10.1093/bioinformatics/btae700).
-Detailled documentation is made available at: [https://pytximport.readthedocs.io](https://pytximport.readthedocs.io/en/latest/start.html).
+Detailled documentation is made available at: [https://pytximport.complextissue.com](https://pytximport.complextissue.com/en/latest/start.html).
 
 ## Installation
 
@@ -142,7 +142,7 @@ To set up `pytximport` for development on your machine, we recommend to git clon
 ```bash
 git clone --depth 1 -b dev https://github.com/complextissue/pytximport.git
 cd pytximport
-pyenv local 3.9
+pyenv local 3.12
 make create-venv
 source .venv/source/activate
 make install-dev

docs/Makefile

@@ -10,12 +10,22 @@ help:
 # cp ../README.md ./source/introduction.md
 build-docs:
 	@./install.sh
-	rm -rf build
 	make html
 
 .PHONY: help Makefile
 
+reset-build:
+	if [ -d ./build/doctrees ]; then \
+        rm -r ./build/doctrees; \
+    fi && \
+    if [ -d ./build/html ]; then \
+        rm -r ./build/html; \
+    fi && \
+    mkdir -p ./build/doctrees && \
+    mkdir -p ./build/html
+
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
+	make reset-build
 	sphinx-build -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/source/conf.py

@@ -37,6 +37,7 @@
     "sphinx.ext.autodoc",
     "sphinx.ext.intersphinx",
     "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
     "sphinx.ext.githubpages",
     "sphinx_copybutton",
     "sphinx_design",

docs/source/example.ipynb

@@ -513,12 +513,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "import numpy as np\n",
     "import pandas as pd\n",
+    "\n",
     "from pytximport import tximport"
    ]
   },
@@ -1813,14 +1814,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
+    "import decoupler as dc\n",
     "from pydeseq2.dds import DeseqDataSet\n",
     "from pydeseq2.default_inference import DefaultInference\n",
-    "from pydeseq2.ds import DeseqStats\n",
-    "import decoupler as dc"
+    "from pydeseq2.ds import DeseqStats"
    ]
   },
   {

docs/source/installation.md

@@ -3,7 +3,7 @@
 :::{card}
 :class-card: sd-bg-warning
 :class-body: sd-bg-text-warning
-**pytximport** only supports Python versions greater than or equal to **3.9**.
+**pytximport** only supports Python versions greater than or equal to **3.10**.
 :::
 
 :::{card} Recommendation
@@ -56,7 +56,7 @@ Install `pytximport` from source:
 ```bash
 git clone --depth 1 -b dev https://github.com/complextissue/pytximport.git
 cd pytximport
-pyenv local 3.9
+pyenv local 3.12
 make create-venv
 source .venv/source/activate
 make install-dev

docs/source/start.md

@@ -5,21 +5,21 @@
 [![Version](https://img.shields.io/pypi/v/pytximport)](https://pypi.org/project/pytximport/)
 [![License](https://img.shields.io/pypi/l/pytximport)](https://github.com/complextissue/pytximport)
 ![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/complextissue/pytximport/ci.yml)
-[![Documentation Status](https://readthedocs.org/projects/pytximport/badge/?version=latest)](https://pytximport.readthedocs.io/en/latest/?badge=latest)
+[![Documentation Status](https://readthedocs.org/projects/pytximport/badge/?version=latest)](https://pytximport.complextissue.com/en/latest/?badge=latest)
 [![Codecov](https://codecov.io/gh/complextissue/pytximport/graph/badge.svg?token=M9JEHJVXYI)](https://codecov.io/gh/complextissue/pytximport)
 [![Install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/pytximport/README.html)
 ![Conda Downloads](https://img.shields.io/conda/d/bioconda/pytximport)
 ![Pepy Total Downloads](https://img.shields.io/pepy/dt/pytximport?label=PyPi%7Cdownloads)
 [![Python Version Required](https://img.shields.io/pypi/pyversions/pytximport)](https://pypi.org/project/pytximport/)
-[![Code Style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
 
 `pytximport` is a Python package for efficient (gene-)count estimation from transcript quantification files produced by pseudoalignment/quasi-mapping tools such as `salmon`, `kallisto`, `rsem` and others. `pytximport` is a port of the popular [tximport Bioconductor R package](https://bioconductor.org/packages/release/bioc/html/tximport.html).
 
 ## Manuscript & Documentation
 
 The pytximport manuscript can be accessed at: [https://doi.org/10.1093/bioinformatics/btae700](https://doi.org/10.1093/bioinformatics/btae700).
-Detailled documentation is made available at: [https://pytximport.readthedocs.io](https://pytximport.readthedocs.io/en/latest/start.html).
+Detailled documentation is made available at: [https://pytximport.complextissue.com](https://pytximport.complextissue.com/en/latest/start.html).
 
 ## Installation
 
@@ -129,7 +129,7 @@ To set up `pytximport` for development on your machine, we recommend to git clon
 ```bash
 git clone --depth 1 -b dev https://github.com/complextissue/pytximport.git
 cd pytximport
-pyenv local 3.9
+pyenv local 3.12
 make create-venv
 source .venv/source/activate
 make install-dev