(fix): run on all files

ilan-gold · ilan-gold · commit ce03c3b166dd · 2024-05-07T15:23:03.000+02:00
diff --git a/.coveragerc_omit b/.coveragerc_omit
@@ -10,4 +10,4 @@ omit =
     vitessce/data_utils/anndata.py
     vitessce/data_utils/ome.py
     vitessce/data_utils/entities.py
-    vitessce/data_utils/multivec.py
+    vitessce/data_utils/multivec.py
diff --git a/.coveragerc_real b/.coveragerc_real
@@ -1,3 +1,2 @@
 [report]
 exclude_lines =
-  
diff --git a/.envrc b/.envrc
@@ -1 +1 @@
-use conda vitessce-python-dev
+use conda vitessce-python-dev
diff --git a/README.md b/README.md
@@ -115,7 +115,7 @@ vw = vc.widget(proxy=True)
 vw
 ```
 
-or 
+or
 
 ```py
 vc.display(proxy=True, host_name="http://localhost:8888")
diff --git a/binder/environment.yml b/binder/environment.yml
@@ -15,4 +15,4 @@ dependencies:
  - pip:
    - loompy
    - scanpy
-   - vitessce[all]
+   - vitessce[all]
diff --git a/demos/.envrc b/demos/.envrc
@@ -1 +1 @@
-use conda vitessce-python-demos
+use conda vitessce-python-demos
diff --git a/demos/README.md b/demos/README.md
@@ -1,6 +1,6 @@
 ## Processing scripts for Vitessce demo datasets
 
-Previously, we developed custom processing scripts for Vitessce demo data in the `vitessce-data` repository. 
+Previously, we developed custom processing scripts for Vitessce demo data in the `vitessce-data` repository.
 
 However, now that there are consensus single-cell file formats (e.g., h5ad) and an ecosystem of data processing packages in the community, we aim to leverage those. Writing demo dataset processing code using Scanpy and AnnData in small Snakemake workflows in this repository should allow us to iterate more quickly and share more demos.
 
@@ -91,4 +91,4 @@ Configure the Google Cloud CLI by running `gcloud auth login` ([reference](https
 
 ```sh
 snakemake --cores all --rerun-triggers mtime --config upload=true
-```
+```
diff --git a/demos/Snakefile b/demos/Snakefile
@@ -26,7 +26,7 @@ subworkflow codeluppi_2018:
 subworkflow codeluppi_2018_via_zarr:
     workdir:
         "codeluppi-2018-via-zarr"
-        
+
 subworkflow combat_2022:
     workdir:
         "combat-2022"
@@ -131,4 +131,4 @@ rule fill_templates:
         for subworkflow_dir in params.subworkflow_dirs:
             if os.path.exists(os.path.join(subworkflow_dir, 'vitessce.template.json')):
                 shell(f"python fill_template.py -d {subworkflow_dir} -t local > {os.path.join(subworkflow_dir, 'vitessce.local.json')}")
-                shell(f"python fill_template.py -d {subworkflow_dir} -t remote -v {BUCKET_VERSION} > {os.path.join(subworkflow_dir, 'vitessce.remote.json')}")
+                shell(f"python fill_template.py -d {subworkflow_dir} -t remote -v {BUCKET_VERSION} > {os.path.join(subworkflow_dir, 'vitessce.remote.json')}")
diff --git a/demos/codeluppi-2018-via-zarr/vitessce.template.json b/demos/codeluppi-2018-via-zarr/vitessce.template.json
@@ -238,4 +238,4 @@
       "h": 2
     }
   ]
-}
+}
diff --git a/demos/codeluppi-2018/Snakefile b/demos/codeluppi-2018/Snakefile
@@ -129,4 +129,4 @@ rule download_molecules_hdf5:
     shell:
         '''
         curl -L --retry 999 --retry-delay 3 -C - -o {output} {params.file_url}
-        '''
+        '''
diff --git a/demos/codeluppi-2018/vitessce.template.json b/demos/codeluppi-2018/vitessce.template.json
@@ -276,4 +276,4 @@
       "h": 2
     }
   ]
-}
+}
diff --git a/demos/combat-2022/Snakefile b/demos/combat-2022/Snakefile
@@ -35,4 +35,3 @@ rule download_data:
         '''
         curl -L --retry 999 --retry-delay 3 -C - -o {output} {params.file_url}
         '''
-
diff --git a/demos/combat-2022/config.yml b/demos/combat-2022/config.yml
@@ -1,2 +1,2 @@
 output:
-- combat_2022_cell.h5ad.zarr
+- combat_2022_cell.h5ad.zarr
diff --git a/demos/combat-2022/vitessce.template.json b/demos/combat-2022/vitessce.template.json
@@ -204,4 +204,4 @@
       "uid": "G"
     }
   ]
-}
+}
diff --git a/demos/common.smk b/demos/common.smk
@@ -14,4 +14,4 @@ def flatten(l):
   return [item for sublist in l for item in sublist]
 
 def is_aws(output_path):
-  return not output_path.endswith('.ome.zarr')
+  return not output_path.endswith('.ome.zarr')
diff --git a/demos/create_demo.sh b/demos/create_demo.sh
@@ -35,4 +35,4 @@ Add the following to the main demos Snakefile:
 subworkflow $SUBWORKFLOW_KEY:
     workdir:
         "$SUBWORKFLOW_DIR"
-EOF
+EOF
diff --git a/demos/eng-2019/Snakefile b/demos/eng-2019/Snakefile
@@ -33,4 +33,4 @@ rule download_file:
     shell:
         '''
         curl -L -o {output} {BASE_URL}.{wildcards.prefix}.json
-        '''
+        '''
diff --git a/demos/eng-2019/vitessce.template.json b/demos/eng-2019/vitessce.template.json
@@ -191,4 +191,4 @@
       "h": 4
     }
   ]
-}
+}
diff --git a/demos/environment.yml b/demos/environment.yml
@@ -28,4 +28,4 @@ dependencies:
    - generate-tiff-offsets>=0.1.7
    - obonet==0.2.5
    - leidenalg
-   - ome-zarr==0.2.1
+   - ome-zarr==0.2.1
diff --git a/demos/habib-2017/Snakefile b/demos/habib-2017/Snakefile
@@ -35,4 +35,3 @@ rule download_data:
         '''
         curl -L -o {output} {params.file_url}
         '''
-
diff --git a/demos/habib-2017/config.yml b/demos/habib-2017/config.yml
@@ -1,2 +1,2 @@
 output:
-- habib_2017_nature_methods.h5ad.zarr
+- habib_2017_nature_methods.h5ad.zarr
diff --git a/demos/habib-2017/vitessce.template.json b/demos/habib-2017/vitessce.template.json
@@ -120,4 +120,4 @@
       "uid": "F"
     }
   ]
-}
+}
diff --git a/demos/human-lymph-node-10x-visium/Snakefile b/demos/human-lymph-node-10x-visium/Snakefile
@@ -20,4 +20,3 @@ rule create_zarr:
             -oa {output.adata} \
             -oi {output.img}
         '''
-
diff --git a/demos/human-lymph-node-10x-visium/config.yml b/demos/human-lymph-node-10x-visium/config.yml
@@ -1,3 +1,3 @@
 output:
 - human_lymph_node_10x_visium.h5ad.zarr
-- human_lymph_node_10x_visium.ome.zarr
+- human_lymph_node_10x_visium.ome.zarr
diff --git a/demos/human-lymph-node-10x-visium/vitessce.template.json b/demos/human-lymph-node-10x-visium/vitessce.template.json
@@ -197,4 +197,4 @@
       "x": 4, "y": 6, "w": 2, "h": 6
     }
   ]
-}
+}
diff --git a/demos/kuppe-2022/Snakefile b/demos/kuppe-2022/Snakefile
@@ -122,4 +122,4 @@ rule download_atac:
     shell:
         '''
         curl -L --retry 999 --retry-delay 3 -C - -o {output} "{params.file_url}"
-        '''
+        '''
diff --git a/demos/kuppe-2022/config.yml b/demos/kuppe-2022/config.yml
@@ -3,4 +3,4 @@ output:
 - kuppe_2022_nature.atac.h5ad.zarr
 - kuppe_2022_nature.joint.h5ad.zarr
 - kuppe_2022_nature.visium.h5ad.zarr
-- kuppe_2022_nature.visium.ome.zarr
+- kuppe_2022_nature.visium.ome.zarr
diff --git a/demos/kuppe-2022/vitessce.template.json b/demos/kuppe-2022/vitessce.template.json
@@ -351,4 +351,4 @@
       "uid": "I"
     }
   ]
-}
+}
diff --git a/demos/marshall-2022/Snakefile b/demos/marshall-2022/Snakefile
@@ -38,4 +38,4 @@ rule download_adata:
     shell:
         '''
         curl -L -o {output} "{params.file_url}"
-        '''
+        '''
diff --git a/demos/marshall-2022/vitessce.template.json b/demos/marshall-2022/vitessce.template.json
@@ -149,4 +149,4 @@
       "uid": "H"
     }
   ]
-}
+}
diff --git a/demos/meta-2022-azimuth/vitessce.template.json b/demos/meta-2022-azimuth/vitessce.template.json
@@ -116,7 +116,7 @@
       },
       "uid": "C"
     },
-    
+
     {
       "component": "featureList",
       "h": 6,
@@ -137,4 +137,4 @@
       "uid": "F"
     }
   ]
-}
+}
diff --git a/demos/satija-2020/Snakefile b/demos/satija-2020/Snakefile
@@ -100,4 +100,4 @@ rule download_cl_obo:
     shell:
         '''
         curl -L -o {output} {params.file_url}
-        '''
+        '''
diff --git a/demos/satija-2020/vitessce.template.json b/demos/satija-2020/vitessce.template.json
@@ -132,4 +132,4 @@
       "y": 4
     }
   ]
-}
+}
diff --git a/demos/sn-atac-seq-hubmap-2020/Snakefile b/demos/sn-atac-seq-hubmap-2020/Snakefile
@@ -32,4 +32,4 @@ rule download_file:
     shell:
         '''
         curl -L -o {output} {BASE_URL}.{wildcards.prefix}.json
-        '''
+        '''
diff --git a/demos/sn-atac-seq-hubmap-2020/vitessce.template.json b/demos/sn-atac-seq-hubmap-2020/vitessce.template.json
@@ -84,4 +84,4 @@
     }
   ],
   "initStrategy": "auto"
-}
+}
diff --git a/demos/wang-2018/Snakefile b/demos/wang-2018/Snakefile
@@ -41,4 +41,4 @@ rule download_file:
     shell:
         '''
         curl -L -o {output} {BASE_URL}.{wildcards.prefix}.json
-        '''
+        '''
diff --git a/demos/wang-2018/vitessce.template.json b/demos/wang-2018/vitessce.template.json
@@ -97,4 +97,4 @@
       "h": 2
     }
   ]
-}
+}
diff --git a/docs/_static/stylesheet.css b/docs/_static/stylesheet.css
@@ -36,4 +36,4 @@ legend {
     z-index: 201;
     text-align: center;
     margin: 0 auto;
-}
+}
diff --git a/docs/api_data.rst b/docs/api_data.rst
@@ -30,4 +30,4 @@ vitessce.data_utils
 .. automodule:: vitessce.data_utils.ome
  :members:
 .. automodule:: vitessce.data_utils.anndata
- :members:
+ :members:
diff --git a/docs/data_examples.rst b/docs/data_examples.rst
@@ -7,4 +7,4 @@ Data preparation examples
 
    notebooks/data_export_s3
    notebooks/data_export_files
-   notebooks/widget_brain_with_base_dir
+   notebooks/widget_brain_with_base_dir
diff --git a/docs/data_options.rst b/docs/data_options.rst
@@ -105,6 +105,3 @@ Jupyter process: remote service like Colab/Binder; Files: remote & accessed via
 ===================================================================================
 
 Unfortunately, this will not work because the remote server cannot access the files that are on another machine behind SSH.
-
-
-
diff --git a/docs/notebooks/.envrc b/docs/notebooks/.envrc
@@ -1 +1 @@
-use conda vitessce-python-notebooks
+use conda vitessce-python-notebooks
diff --git a/docs/notebooks/environment.yml b/docs/notebooks/environment.yml
@@ -21,4 +21,4 @@ dependencies:
  - pip
  - pip:
    - loompy>=3.0.6
-   - scikit-misc>=0.1.3
+   - scikit-misc>=0.1.3
diff --git a/docs/widget_examples.rst b/docs/widget_examples.rst
@@ -10,4 +10,4 @@ Widget examples
    notebooks/widget_pbmc
    notebooks/widget_loom
    notebooks/widget_from_dict
-   notebooks/widget_pbmc_remote.ipynb
+   notebooks/widget_pbmc_remote.ipynb
diff --git a/pytest.ini b/pytest.ini
@@ -1,2 +1,2 @@
 [pytest]
-addopts = --doctest-modules --verbose --ignore=docs --ignore=demos
+addopts = --doctest-modules --verbose --ignore=docs --ignore=demos
diff --git a/setup.cfg b/setup.cfg
@@ -16,4 +16,4 @@ exclude =
   ./js/node_modules/,
   ./docs/notebooks/.ipynb_checkpoints/,
   ./build/,
-  ./.ipynb_checkpoints/
+  ./.ipynb_checkpoints/
diff --git a/tests/data/test.ome.zarr/.zgroup b/tests/data/test.ome.zarr/.zgroup
@@ -1,3 +1,3 @@
 {
     "zarr_format": 2
-}
+}

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,2 @@`
`1`	`1`	`[report]`
`2`	`2`	`exclude_lines =`
`3`		`-`
Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-use conda vitessce-python-dev`
	`1`	`+use conda vitessce-python-dev`
Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-use conda vitessce-python-demos`
	`1`	`+use conda vitessce-python-demos`
Original file line number	Diff line number	Diff line change
`@@ -238,4 +238,4 @@`
`238`	`238`	`"h": 2`
`239`	`239`	`}`
`240`	`240`	`]`
`241`		`-}`
	`241`	`+}`
-Original file line number
+Diff line change
     shell:
         '''
         curl -L --retry 999 --retry-delay 3 -C - -o {output} {params.file_url}
 -        '''
 +        '''