PyPI - cell-data-loader - Versions diffs - 0.0.6__tar.gz → 0.0.8__tar.gz - Mend

cell-data-loader 0.0.6tar.gz → 0.0.8tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (501) hide show

cell_data_loader-0.0.8/.github/workflows/publish-to-pypi.yml ADDED Viewed

@@ -0,0 +1,95 @@
+name: Publish Python 🐍 distribution 📦 to PyPI and TestPyPI
+on: push
+jobs:
+  build:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.x"
+    - name: Install pypa/build
+      run: >-
+        python3 -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+  publish-to-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to PyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/cell-data-loader  # Replace <package-name> with your PyPI project name
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+  github-release:
+    name: >-
+      Sign the Python 🐍 distribution 📦 with Sigstore
+      and upload them to GitHub Release
+    needs:
+    - publish-to-pypi
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write  # IMPORTANT: mandatory for making GitHub Releases
+      id-token: write  # IMPORTANT: mandatory for sigstore
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Sign the dists with Sigstore
+      uses: sigstore/gh-action-sigstore-python@v2.1.1
+      with:
+        inputs: >-
+          ./dist/*.tar.gz
+          ./dist/*.whl
+    - name: Create GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      run: >-
+        gh release create
+        '${{ github.ref_name }}'
+        --repo '${{ github.repository }}'
+        --notes ""
+    - name: Upload artifact signatures to GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      # Upload to GitHub Release using the `gh` CLI.
+      # `dist/` contains the built packages, and the
+      # sigstore-produced signatures and certificates.
+      run: >-
+        gh release upload
+        '${{ github.ref_name }}' dist/**
+        --repo '${{ github.repository }}'

{cell_data_loader-0.0.6 → cell_data_loader-0.0.8}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: cell_data_loader
-Version: 0.0.6
+Version: 0.0.8
 Summary: Converts general images of cells into formats and labels for deep learning pipelines
 Project-URL: Homepage, https://github.com/mleming/CellDataLoader
 Author-email: Matt Leming <mleming@mgh.harvard.edu>
@@ -15,7 +15,7 @@ Requires-Dist: scikit-image
 Requires-Dist: scipy
 Requires-Dist: slideio==2.4.1
 Requires-Dist: torch
-Requires-Dist: torchvision
+Requires-Dist: torchvision<=0.15.0
 Description-Content-Type: text/markdown
 Cell Data Loader
@@ -86,6 +86,20 @@ for label,image in dataloader:
 	...
 ~~~
+Boxes
+-----
+In cases where you need to cut out individual cells from an image and have the coordinates file, cell_data_loader.py accepts an argument, cell_box_filelist, which is a list of files corresponding to the inputs that mark out the coordinates of labels on the cells. The format of the csv is as follows:
+| X  | Y   | W  | H | Label |
+| -  | -   | -  | - | ----- |
+| 14 | 13  | 5  | 6 | 0     |
+| 20 | 25  | 15 | 5 | 1     |
+~~~python
+dataloader = CellDataloader('/path/to/file.svs',cell_box_filelist=['/path/to/boxfile.csv'])
+~~~
 Arguments
 ---------

{cell_data_loader-0.0.6 → cell_data_loader-0.0.8}/README.md RENAMED Viewed

@@ -66,6 +66,20 @@ for label,image in dataloader:
 	...
 ~~~
+Boxes
+-----
+In cases where you need to cut out individual cells from an image and have the coordinates file, cell_data_loader.py accepts an argument, cell_box_filelist, which is a list of files corresponding to the inputs that mark out the coordinates of labels on the cells. The format of the csv is as follows:
+| X  | Y   | W  | H | Label |
+| -  | -   | -  | - | ----- |
+| 14 | 13  | 5  | 6 | 0     |
+| 20 | 25  | 15 | 5 | 1     |
+~~~python
+dataloader = CellDataloader('/path/to/file.svs',cell_box_filelist=['/path/to/boxfile.csv'])
+~~~
 Arguments
 ---------

cell_data_loader-0.0.8/data/3368914_4_non_tumor/ny=45056_nx=35840.jpg ADDED Viewed

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:70a0ed6b9fe9251a00a075c720a26010863374682c221886fc0688a0109f79ad
+size 60054

cell_data_loader-0.0.8/data/4173633_5/4173633_5.svs ADDED Viewed

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:35b57d5926306a1ac8c28a1e5683f631f79a2c4124a89f59aac63b561757d3c2
+size 292401047