Sc 38 release (#75)

* SC_38 rename * SC_38 rename * update notebooks * SC_38 release * SC_38 release * SC_38 release * SC_38 prepare release * SC_38 prepare release
saeyslab · Dec 9, 2024 · 5f6dd4d · 5f6dd4d
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diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
@@ -0,0 +1,42 @@
+name: build
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches: [main]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout Code
+      uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.12'
+        cache: "pip"
+        cache-dependency-path: "**/setup.cfg"
+
+    - name: Install Build Dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools wheel build twine
+
+    - name: Build Package
+      run: |
+        python -m build
+
+    #- name: Upload Build Artifacts
+    #  uses: actions/upload-artifact@v3
+    #  with:
+    #    name: dist-artifacts
+    #    path: dist/
+
+
+    - name: Check Package
+      run: |
+        twine check --strict dist/*
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
@@ -0,0 +1,31 @@
+name: Release
+
+on:
+    release:
+        types: [published]
+
+jobs:
+    release:
+        # requires that you have put your twine API key in your
+        # github secrets
+        runs-on: ubuntu-latest
+        if: contains(github.ref, 'tags')
+        steps:
+            - name: Checkout code
+              uses: actions/checkout@v3
+
+            - name: Set up Python 3.12
+              uses: actions/setup-python@v4
+              with:
+                  python-version: "3.12"
+
+            - name: Install hatch
+              run: pip install hatch
+
+            - name: Build project for distribution
+              run: hatch build
+
+            - name: Publish a Python distribution to PyPI
+              uses: pypa/gh-action-pypi-publish@release/v1
+              with:
+                  password: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -3,17 +3,18 @@ name: Run tests
 on:
   workflow_dispatch:
 
-  push:
-    branches:
-      - main
+# skip automatic testing
+  #push:
+  #  branches:
+  #    - main
 
-    #pull_request:
-    #  branches:
-    #    - main
+  #pull_request:
+  #  branches:
+  #    - main
 
-    paths:
-      - "src/sparrow/**"
-      - ".github/workflows/run_tests.yml"
+  #  paths:
+  #    - "src/harpy/**"
+  #    - ".github/workflows/run_tests.yml"
 
 env:
   CACHE_NUMBER: 1 # increase to reset cache manually
@@ -37,7 +38,7 @@ jobs:
         with:
           miniforge-variant: Mambaforge
           miniforge-version: latest
-          activate-environment: napari-sparrow
+          activate-environment: harpy
           use-mamba: true
           python-version: ${{ matrix.python-version }}
 
@@ -58,17 +59,17 @@ jobs:
         id: cache
 
       - name: Update environment
-        run: mamba env update -n napari-sparrow -f environment.yml
+        run: mamba env update -n harpy -f environment.yml
         if: steps.cache.outputs.cache-hit != 'true'
 
       # this runs the platform-specific tests declared in tox.ini
       - name: Test with tox
         shell: bash -l {0}
         run: |
-          conda activate napari-sparrow
+          conda activate harpy
           pip install -e '.[testing]'
-          pip install tox tox-gh-actions
-          tox
+          pytest --ignore=src/harpy/_tests/test_widget.py --color=yes --cov=dummy --cov-config=pyproject.toml --cov-report=xml --cov-report=term-missing
+
         env:
           PLATFORM: ${{ matrix.os }}
 

diff --git a/README.md b/README.md
@@ -1,14 +1,15 @@
 <!-- These badges won't work while the GitHub repo is private:
-[![License BSD-3](https://img.shields.io/pypi/l/napari-sparrow.svg?color=green)](https://github.com/saeyslab/napari-sparrow/raw/main/LICENSE)
-[![PyPI](https://img.shields.io/pypi/v/napari-sparrow.svg?color=green)](https://pypi.org/project/napari-sparrow)
+[![License BSD-3](https://img.shields.io/pypi/l/harpy.svg?color=green)](https://github.com/saeyslab/harpy/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/harpy.svg?color=green)](https://pypi.org/project/harpy)
 [![tests](https://github.com/saeyslab/harpy/workflows/tests/badge.svg)](https://github.com/saeyslab/harpy/actions)
-[![Python Version](https://img.shields.io/pypi/pyversions/napari-sparrow.svg?color=green)](https://python.org)
+[![Python Version](https://img.shields.io/pypi/pyversions/harpy.svg?color=green)](https://python.org)
 [![codecov](https://codecov.io/gh/saeyslab/harpy/graph/badge.svg?token=7UXMDWVYFZ)](https://codecov.io/gh/saeyslab/harpy)
-[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-sparrow)](https://napari-hub.org/plugins/napari-sparrow)
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/harpy)](https://napari-hub.org/plugins/harpy)
 -->
 
 # **Harpy: single-cell spatial proteomics analysis that makes you happy** <img src="./docs/_static/img/logo.png" align ="right" alt="" width ="150"/>
 
+![Build Status](https://github.com//saeyslab/harpy/actions/workflows/build.yaml/badge.svg)
 [![documentation badge](https://readthedocs.org/projects/harpy/badge/?version=latest)](https://harpy.readthedocs.io/en/latest/)
 
 Note: This package is still under very active development.
@@ -46,7 +47,7 @@ If you encounter any problems, please [file an issue] along with a detailed desc
 [Cookiecutter]: https://github.com/audreyr/cookiecutter
 [BSD-3]: http://opensource.org/licenses/BSD-3-Clause
 [cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
-[file an issue]: https://github.com/saeyslab/napari-sparrow/issues
+[file an issue]: https://github.com/saeyslab/harpy/issues
 [napari]: https://github.com/napari/napari
 [tox]: https://tox.readthedocs.io/en/latest/
 [pip]: https://pypi.org/project/pip/

diff --git a/docs/api.md b/docs/api.md
@@ -4,9 +4,9 @@
 
 Import Harpy as::
 
-    import sparrow as sp
+    import harpy as hp
 
-.. module:: sparrow
+.. module:: harpy
 ```
 
 ## IO
@@ -15,8 +15,8 @@ I/O.
 
 ```{eval-rst}
 
-.. module:: sparrow.io
-.. currentmodule:: sparrow
+.. module:: harpy.io
+.. currentmodule:: harpy
 
 .. autosummary::
     :toctree: generated
@@ -38,8 +38,8 @@ Operations on image and labels layers.
 
 ```{eval-rst}
 
-.. module:: sparrow.im
-.. currentmodule:: sparrow
+.. module:: harpy.im
+.. currentmodule:: harpy
 
 .. autosummary::
     :toctree: generated
@@ -76,8 +76,8 @@ Operations on shapes (polygons) layers.
 
 ```{eval-rst}
 
-.. module:: sparrow.sh
-.. currentmodule:: sparrow
+.. module:: harpy.sh
+.. currentmodule:: harpy
 
 .. autosummary::
     :toctree: generated
@@ -94,8 +94,8 @@ Operations on table (`AnnData` object) layers.
 
 ```{eval-rst}
 
-.. module:: sparrow.tb
-.. currentmodule:: sparrow
+.. module:: harpy.tb
+.. currentmodule:: harpy
 
 .. autosummary::
     :toctree: generated
@@ -126,8 +126,8 @@ Operations on points (`Dask` `DataFrame` object) layers.
 
 ```{eval-rst}
 
-.. module:: sparrow.pt
-.. currentmodule:: sparrow
+.. module:: harpy.pt
+.. currentmodule:: harpy
 
 .. autosummary::
     :toctree: generated
@@ -143,8 +143,8 @@ Plotting functions.
 
 ```{eval-rst}
 
-.. module:: sparrow.pl
-.. currentmodule:: sparrow
+.. module:: harpy.pl
+.. currentmodule:: harpy
 
 .. autosummary::
     :toctree: generated
@@ -161,8 +161,8 @@ Plotting functions.
 
 ```{eval-rst}
 
-.. module:: sparrow.pl
-.. currentmodule:: sparrow
+.. module:: harpy.pl
+.. currentmodule:: harpy
 
 .. autosummary::
     :toctree: generated
@@ -182,8 +182,8 @@ Plotting functions.
 
 ```{eval-rst}
 
-.. module:: sparrow.pl
-.. currentmodule:: sparrow
+.. module:: harpy.pl
+.. currentmodule:: harpy
 
 .. autosummary::
     :toctree: generated
@@ -204,8 +204,8 @@ Utility functions.
 
 ```{eval-rst}
 
-.. module:: sparrow.utils
-.. currentmodule:: sparrow
+.. module:: harpy.utils
+.. currentmodule:: harpy
 
 .. autosummary::
     :toctree: generated
@@ -219,8 +219,8 @@ Dataset loaders.
 
 ```{eval-rst}
 
-.. module:: sparrow.datasets
-.. currentmodule:: sparrow
+.. module:: harpy.datasets
+.. currentmodule:: harpy
 
 .. autosummary::
     :toctree: generated

diff --git a/docs/conf.py b/docs/conf.py
@@ -16,7 +16,7 @@
 
 # -- Project information -----------------------------------------------------
 
-info = metadata("sparrow")
+info = metadata("harpy-analysis")
 project_name = info["Name"]
 author = "SaeysLab"
 copyright = f"{datetime.now():%Y}, {author}"

diff --git a/docs/index.md b/docs/index.md
@@ -50,7 +50,7 @@ Please read our documentation to learn more.
 
 ```
 
-The Harpy Python package described here builds on the spatial transcriptomics analysis tool [SPArrOW](https://github.com/saeyslab/napari-sparrow) and keeps the package name for compatibility.
+The Harpy Python package described here builds on the spatial transcriptomics analysis tool [SPArrOW](https://github.com/saeyslab/napari-sparrow).
 
 For spatial proteomics analysis, cite [the Harpy GitHub repository](https://github.com/saeyslab/harpy).
 

diff --git a/docs/installation.md b/docs/installation.md
@@ -13,7 +13,7 @@ mamba env update -f environment.yml --prune
 conda activate harpy
 ```
 
-If you plan to use the `Harpy` function `sp.im.tiling_correction`, please install `jax` and `basicpy`. On Mac and Linux, this can be done via `pip install ...`, on Windows you will have to run the following commands:
+If you plan to use the `Harpy` function `harpy.im.tiling_correction`, please install `jax` and `basicpy`. On Mac and Linux, this can be done via `pip install ...`, on Windows you will have to run the following commands:
 
 ```bash
 pip install "jax[cpu]" -f https://whls.blob.core.windows.net/unstable/index.html --use-deprecated legacy-resolver
@@ -35,19 +35,19 @@ pip install git+https://github.com/saeyslab/harpy.git
 To use the plugin, run
 
 ```bash
-pip install "git+https://github.com/saeyslab/harpy.git#egg=sparrow[plugin]"
+pip install "git+https://github.com/saeyslab/harpy.git#egg=harpy[plugin]"
 ```
 
 To run `Harpy` from the `cli`:
 
 ```bash
-pip install "git+https://github.com/saeyslab/harpy.git#egg=sparrow[cli]"
+pip install "git+https://github.com/saeyslab/harpy.git#egg=harpy[cli]"
 ```
 
 To be able to run the unit tests:
 
 ```bash
-pip install "git+https://github.com/saeyslab/harpy.git#egg=sparrow[testing]"
+pip install "git+https://github.com/saeyslab/harpy.git#egg=harpy[testing]"
 ```
-Original file line number
+Diff line change
@@ Expand Up / @@ -50,7 +50,7 @@ Please read our documentation to learn more. @@
     ```
-    The Harpy Python package described here builds on the spatial transcriptomics analysis tool [SPArrOW](https://github.com/saeyslab/napari-sparrow) and keeps the package name for compatibility.
+    The Harpy Python package described here builds on the spatial transcriptomics analysis tool [SPArrOW](https://github.com/saeyslab/napari-sparrow).
     For spatial proteomics analysis, cite [the Harpy GitHub repository](https://github.com/saeyslab/harpy).
@@ Expand Down @@