run pre-commit

.github/ISSUE_TEMPLATE/custom.md

@@ -6,5 +6,3 @@ labels: ''
 assignees: ''
 
 ---
-
-

.gitignore

@@ -100,4 +100,4 @@ coverage.xml
 *.cover
 *.py,cover
 .hypothesis/
-.pytest_cache/
+.pytest_cache/

.pre-commit-config.yaml

@@ -25,6 +25,3 @@ repos:
           - id: end-of-file-fixer
           - id: check-yaml
           - id: debug-statements
-          - id: double-quote-string-fixer
-          - id: name-tests-test
-          - id: requirements-txt-fixer

LICENSE

@@ -26,4 +26,4 @@ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -108,4 +108,4 @@ Our article is not published yet. In the meantime, you can cite our [preprint](h
     eprint = {https://www.biorxiv.org/content/early/2023/12/23/2023.12.22.571863.full.pdf},
     journal = {bioRxiv}
 }
-```
+```

docs/api/_sdata.md

@@ -23,4 +23,4 @@
 
 ::: sopa._sdata.get_spatial_image
     options:
-      show_root_heading: true
+      show_root_heading: true

docs/api/annotation/fluorescence.md

@@ -4,4 +4,4 @@
 
 ::: sopa.annotation.preprocess_fluo
     options:
-      show_root_heading: true
+      show_root_heading: true

docs/api/annotation/tangram.md

@@ -1,3 +1,3 @@
 ::: sopa.annotation.tangram.tangram_annotate
     options:
-      show_root_heading: true
+      show_root_heading: true

docs/api/io.explorer.md

@@ -33,11 +33,11 @@
 ::: sopa.io.explorer.str_cell_id
     options:
       show_root_heading: true
-    
+
 ::: sopa.io.explorer.align
     options:
       show_root_heading: true
 
 ::: sopa.io.explorer.save_column_csv
     options:
-      show_root_heading: true
+      show_root_heading: true

docs/api/io.md

@@ -30,4 +30,4 @@
 
 ::: sopa.io.ome_tif
     options:
-      show_root_heading: true
+      show_root_heading: true

docs/api/segmentation/aggregate.md

@@ -16,4 +16,4 @@
 
 ::: sopa.segmentation.aggregate.Aggregator
     options:
-      show_root_heading: true
+      show_root_heading: true

docs/api/segmentation/baysor.md

@@ -1,3 +1,3 @@
 ::: sopa.segmentation.baysor.resolve.resolve
     options:
-      show_root_heading: true
+      show_root_heading: true

docs/api/segmentation/methods.md

@@ -1,3 +1,3 @@
 ::: sopa.segmentation.methods.cellpose_patch
     options:
-      show_root_heading: true
+      show_root_heading: true

docs/api/segmentation/patching.md

@@ -1,3 +1,3 @@
 ::: sopa.segmentation.patching.Patches2D
     options:
-      show_root_heading: true
+      show_root_heading: true

docs/api/segmentation/stainings.md

@@ -1,3 +1,3 @@
 ::: sopa.segmentation.stainings.StainingSegmentation
     options:
-      show_root_heading: true
+      show_root_heading: true

docs/api/utils/data.md

@@ -4,4 +4,4 @@
 
 ::: sopa.utils.data.blobs
     options:
-      show_root_heading: true
+      show_root_heading: true

docs/api/utils/image.md

@@ -8,4 +8,4 @@
 
 ::: sopa.utils.image.resize_numpy
     options:
-      show_root_heading: true
+      show_root_heading: true

docs/cite_us.md

@@ -17,4 +17,4 @@ Our article is not published yet. In the meantime, you can cite our [preprint](h
 This library has been developed by Quentin Blampey, PhD student in Biomathematics / Deep Learning. The following institutions funded this work:
 
 - Lab of Mathematics and Computer Science (MICS), **CentraleSupélec** (Engineering School, Paris-Saclay University).
-- PRISM center, **Gustave Roussy Institute** (Cancer campus, Paris-Saclay University).
+- PRISM center, **Gustave Roussy Institute** (Cancer campus, Paris-Saclay University).

docs/cli.md

@@ -11,7 +11,7 @@ When installing `sopa` as written in our [getting-started guidelines](../getting
 ```console
 // Run the Sopa CLI helper
 $ sopa --help
- Usage: sopa [OPTIONS] COMMAND [ARGS]...    
+ Usage: sopa [OPTIONS] COMMAND [ARGS]...
 ╭─ Commands ─────────────────────────────────────────────────────╮
 │ aggregate     Aggregate transcripts/channels inside cells      │
 │ annotate      Perform cell-type annotation                     │

docs/css/custom.css

@@ -6,4 +6,4 @@
 
 .termy [data-termynal] {
     white-space: pre-wrap;
-}
+}

docs/css/termynal.css

@@ -107,4 +107,4 @@ a[data-terminal-control] {
     50% {
         opacity: 0;
     }
-}
+}

docs/js/custom.js

@@ -102,4 +102,4 @@ function loadVisibleTermynals() {
 }
 window.addEventListener("scroll", loadVisibleTermynals);
 createTermynals();
-loadVisibleTermynals();
+loadVisibleTermynals();

docs/js/mathjax.js

@@ -10,8 +10,7 @@ window.MathJax = {
       processHtmlClass: "arithmatex"
     }
   };
-  
-  document$.subscribe(() => { 
+
+  document$.subscribe(() => {
     MathJax.typesetPromise()
   })
-

docs/js/termynal.js

@@ -261,4 +261,4 @@ if (document.currentScript.hasAttribute('data-termynal-container')) {
     const containers = document.currentScript.getAttribute('data-termynal-container');
     containers.split('|')
         .forEach(container => new Termynal(container))
-}
+}

docs/tutorials/advanced_segmentation.md

@@ -173,7 +173,7 @@ def dummy_method(**method_kwargs):
 
 ### 2. Setup
 
-To use the CLI, you'll need to clone the repository. Also, we recommend installing Sopa in dev mode, allowing you to update your segmentation function without re-installing everything. For instance: 
+To use the CLI, you'll need to clone the repository. Also, we recommend installing Sopa in dev mode, allowing you to update your segmentation function without re-installing everything. For instance:
 
 ```sh
 git clone https://github.com/gustaveroussy/sopa.git

docs/tutorials/cli_usage.md

@@ -300,4 +300,4 @@ import spatialdata
 sdata = spatialdata.read_zarr("tuto.zarr")
 ```
 - You can use [Squidpy](https://squidpy.readthedocs.io/en/latest/index.html) which operates on both the `SpatialData` object or the `AnnData` object, or use other tools of the `scverse` ecosystem such as [`Scanpy`](https://scanpy.readthedocs.io/en/stable/index.html).
-- You can also use the file `tuto.explorer/adata.h5ad` if you prefer the `AnnData` object instead of the full `SpatialData` object.
+- You can also use the file `tuto.explorer/adata.h5ad` if you prefer the `AnnData` object instead of the full `SpatialData` object.

mkdocs.yml

@@ -68,4 +68,4 @@ extra_javascript:
   - js/custom.js
   - js/mathjax.js
   - https://polyfill.io/v3/polyfill.min.js?features=es6
-  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
+  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js

tests/test_rasterize_geometries.py

@@ -28,7 +28,7 @@ def test_raster_and_geometrize():
 
     assert (
         mask == new_mask
-    ).all(), f"Applying geometrize and then rasterize shouldn't change the mask"
+    ).all(), "Applying geometrize and then rasterize shouldn't change the mask"
 
 
 def test_rasterize_cropped():

workflow/Snakefile

@@ -99,7 +99,7 @@ rule patch_segmentation_baysor:
         if command -v module &> /dev/null; then
             module purge
         fi
-        
+
         cd {input.baysor_patch}
         {config[executables][baysor]} run --save-polygons GeoJSON -c config.toml transcripts.csv {params.args_baysor_prior_seg}
         """
@@ -222,4 +222,4 @@ rule explorer:
     shell:
         """
         sopa explorer write {paths.sdata_path} --output-path {paths.explorer_directory} {params.args_explorer} --mode '-i'
-        """
+        """

workflow/config/README.md

@@ -3,4 +3,4 @@
 Snakemake config are `.yaml` files. We provide many examples of such a config in this directory.
 You can choose an existing one (inside the directory corresponding to your technology of interest) or make your own config.
 
-All arguments are detailed in the [`example_commented.yaml`](https://github.com/gustaveroussy/sopa/blob/master/workflow/config/example_commented.yaml) file.
+All arguments are detailed in the [`example_commented.yaml`](https://github.com/gustaveroussy/sopa/blob/master/workflow/config/example_commented.yaml) file.

workflow/config/example_commented.yaml

@@ -1,7 +1,7 @@
 ### This file details all existing Sopa parameters
 ###
 ### Most of these parameters are optional: don't hesitate to delete those that doesn't interest you
-### 
+###
 ### Before creating your own config, you should check if there is not already an existing
 ### config that works for you, see https://github.com/gustaveroussy/sopa/tree/master/workflow/config
 
@@ -102,4 +102,4 @@ explorer: # parameters related to the conversion to the Xenium Explorer (Sopa's
   pixel_size: 0.2125 # [optional] this is the number of microns in a pixel for the technology used (see the config of your technology of interest)
 
 executables:
-  baysor: ~/.julia/bin/baysor # [optional] if you run baysor, write here the path to the 'baysor' executable
+  baysor: ~/.julia/bin/baysor # [optional] if you run baysor, write here the path to the 'baysor' executable

workflow/config/phenocycler/README.md

@@ -2,4 +2,4 @@ For PhenoCycler data, there are multiple config files based on the resolution se
 Choose the right one according to your settings:
 - 10X (1 micron is 1 pixel)
 - 20X (1 micron is 2 pixels)
-- 40X (1 micron is 4 pixels)
+- 40X (1 micron is 4 pixels)

workflow/config/phenocycler/base_10X.yaml

@@ -18,7 +18,7 @@ aggregate:
   average_intensities: true
   min_intensity_ratio: 0.1
   expand_radius_ratio: 0.1
-  
+
 explorer:
   ram_threshold_gb: 8
-  pixel_size: 1
+  pixel_size: 1

workflow/config/phenocycler/base_20X.yaml

@@ -18,7 +18,7 @@ aggregate:
   average_intensities: true
   min_intensity_ratio: 0.1
   expand_radius_ratio: 0.1
-  
+
 explorer:
   ram_threshold_gb: 8
   pixel_size: 0.5

workflow/config/phenocycler/base_40X.yaml

@@ -18,7 +18,7 @@ aggregate:
   average_intensities: true
   min_intensity_ratio: 0.1
   expand_radius_ratio: 0.1
-  
+
 explorer:
   ram_threshold_gb: 8
-  pixel_size: 0.25
+  pixel_size: 0.25

workflow/config/toy/uniform_baysor.yaml

@@ -47,7 +47,7 @@ annotation:
       CK: Tumoral cell
       CD3: T cell
       CD20: B cell
-      
+
 explorer:
   gene_column: "genes"
   ram_threshold_gb: 16

workflow/config/toy/uniform_baysor_overlaps.yaml

@@ -47,7 +47,7 @@ annotation:
       CK: Tumoral cell
       CD3: T cell
       CD20: B cell
-      
+
 explorer:
   gene_column: "genes"
   ram_threshold_gb: 16

workflow/config/xenium/base.yaml

@@ -37,7 +37,7 @@ segmentation:
 
 aggregate:
   average_intensities: true
-  
+
 # Comment this out if you want to use tangram -->
 
 # annotation:

workflow/config/xenium/cellpose_baysor.yaml

@@ -46,7 +46,7 @@ segmentation:
 
 aggregate:
   average_intensities: true
-  
+
 # Comment this out if you want to use tangram -->
 
 # annotation:

workflow/slurm/config.yaml

@@ -20,4 +20,4 @@ keep-going: True
 rerun-incomplete: True
 printshellcmds: True
 scheduler: greedy
-use-conda: True
+use-conda: True

workflow/utils.py

@@ -14,7 +14,7 @@ def sanity_check_config(config: dict):
         "data_path" in config or "sdata_path" in config
     ), "Invalid config. Provide '--config data_path=...' when running the pipeline"
 
-    if "data_path" in config and not "sdata_path" in config:
+    if "data_path" in config and "sdata_path" not in config:
         config["sdata_path"] = Path(config["data_path"]).with_suffix(".zarr")
         print(
             f"SpatialData object path set to default: {config['sdata_path']}\nTo change this behavior, provide `--config sdata_path=...` when running the snakemake pipeline"