(chore): update linting/formatting + pre-commits

.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

.coveragerc_real

@@ -1,3 +1,2 @@
 [report]
 exclude_lines =
-

.envrc

@@ -1 +1 @@
-use conda vitessce-python-dev
+use conda vitessce-python-dev

.pre-commit-config.yaml

@@ -0,0 +1,29 @@
+fail_fast: false
+default_language_version:
+  python: python3
+default_stages:
+  - commit
+  - push
+minimum_pre_commit_version: 2.16.0
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.5
+    hooks:
+      - id: ruff
+        types_or: [python, pyi, jupyter]
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: detect-private-key
+      - id: check-ast
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: trailing-whitespace
+      - id: check-case-conflict
+      # Check that there are no merge conflicts (could be generated by template sync)
+      - id: check-merge-conflict
+        args: [--assume-in-merge]

README.md

@@ -43,24 +43,10 @@ In this repository, there are multiple conda environments for different purposes
 ## Linting and testing
 
 ```sh
-flake8
+pre-commit run --all
 pytest
 ```
 
-### Formatting
-
-One file:
-
-```sh
-autopep8 --in-place --aggressive ./path/to/file.py
-```
-
-All `.py` files:
-
-```sh
-find . -name '*.py' -exec autopep8 --in-place --aggressive '{}' \;
-```
-
 
 ## Documentation
 
@@ -115,7 +101,7 @@ vw = vc.widget(proxy=True)
 vw
 ```
 
-or 
+or
 
 ```py
 vc.display(proxy=True, host_name="http://localhost:8888")

binder/environment.yml

@@ -15,4 +15,4 @@ dependencies:
  - pip:
    - loompy
    - scanpy
-   - vitessce[all]
+   - vitessce[all]

demos/.envrc

@@ -1 +1 @@
-use conda vitessce-python-demos
+use conda vitessce-python-demos

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
-```
+```

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')}")

demos/codeluppi-2018-via-zarr/vitessce.template.json

@@ -238,4 +238,4 @@
       "h": 2
     }
   ]
-}
+}

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}
-        '''
+        '''

demos/codeluppi-2018/vitessce.template.json

@@ -276,4 +276,4 @@
       "h": 2
     }
   ]
-}
+}

demos/combat-2022/Snakefile

@@ -35,4 +35,3 @@ rule download_data:
         '''
         curl -L --retry 999 --retry-delay 3 -C - -o {output} {params.file_url}
         '''
-

demos/combat-2022/config.yml

@@ -1,2 +1,2 @@
 output:
-- combat_2022_cell.h5ad.zarr
+- combat_2022_cell.h5ad.zarr

demos/combat-2022/vitessce.template.json

@@ -204,4 +204,4 @@
       "uid": "G"
     }
   ]
-}
+}

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')

demos/create_demo.sh

@@ -35,4 +35,4 @@ Add the following to the main demos Snakefile:
 subworkflow $SUBWORKFLOW_KEY:
     workdir:
         "$SUBWORKFLOW_DIR"
-EOF
+EOF

demos/eng-2019/Snakefile

@@ -33,4 +33,4 @@ rule download_file:
     shell:
         '''
         curl -L -o {output} {BASE_URL}.{wildcards.prefix}.json
-        '''
+        '''

demos/eng-2019/vitessce.template.json

@@ -191,4 +191,4 @@
       "h": 4
     }
   ]
-}
+}

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

demos/habib-2017/Snakefile

@@ -35,4 +35,3 @@ rule download_data:
         '''
         curl -L -o {output} {params.file_url}
         '''
-

demos/habib-2017/config.yml

@@ -1,2 +1,2 @@
 output:
-- habib_2017_nature_methods.h5ad.zarr
+- habib_2017_nature_methods.h5ad.zarr

demos/habib-2017/vitessce.template.json

@@ -120,4 +120,4 @@
       "uid": "F"
     }
   ]
-}
+}

demos/human-lymph-node-10x-visium/Snakefile

@@ -20,4 +20,3 @@ rule create_zarr:
             -oa {output.adata} \
             -oi {output.img}
         '''
-

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

demos/human-lymph-node-10x-visium/vitessce.template.json

@@ -197,4 +197,4 @@
       "x": 4, "y": 6, "w": 2, "h": 6
     }
   ]
-}
+}

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}"
-        '''
+        '''

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

demos/kuppe-2022/vitessce.template.json

@@ -351,4 +351,4 @@
       "uid": "I"
     }
   ]
-}
+}

demos/marshall-2022/Snakefile

@@ -38,4 +38,4 @@ rule download_adata:
     shell:
         '''
         curl -L -o {output} "{params.file_url}"
-        '''
+        '''

demos/marshall-2022/vitessce.template.json

@@ -149,4 +149,4 @@
       "uid": "H"
     }
   ]
-}
+}

demos/meta-2022-azimuth/vitessce.template.json

@@ -116,7 +116,7 @@
       },
       "uid": "C"
     },
-    
+
     {
       "component": "featureList",
       "h": 6,
@@ -137,4 +137,4 @@
       "uid": "F"
     }
   ]
-}
+}

demos/satija-2020/Snakefile

@@ -100,4 +100,4 @@ rule download_cl_obo:
     shell:
         '''
         curl -L -o {output} {params.file_url}
-        '''
+        '''

demos/satija-2020/vitessce.template.json

@@ -132,4 +132,4 @@
       "y": 4
     }
   ]
-}
+}

demos/sn-atac-seq-hubmap-2020/Snakefile

@@ -32,4 +32,4 @@ rule download_file:
     shell:
         '''
         curl -L -o {output} {BASE_URL}.{wildcards.prefix}.json
-        '''
+        '''

demos/sn-atac-seq-hubmap-2020/vitessce.template.json

@@ -84,4 +84,4 @@
     }
   ],
   "initStrategy": "auto"
-}
+}

demos/wang-2018/Snakefile

@@ -41,4 +41,4 @@ rule download_file:
     shell:
         '''
         curl -L -o {output} {BASE_URL}.{wildcards.prefix}.json
-        '''
+        '''

demos/wang-2018/vitessce.template.json

@@ -97,4 +97,4 @@
       "h": 2
     }
   ]
-}
+}

docs/_static/stylesheet.css

@@ -36,4 +36,4 @@ legend {
     z-index: 201;
     text-align: center;
     margin: 0 auto;
-}
+}

docs/api_data.rst

@@ -30,4 +30,4 @@ vitessce.data_utils
 .. automodule:: vitessce.data_utils.ome
  :members:
 .. automodule:: vitessce.data_utils.anndata
- :members:
+ :members:

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

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.
-
-
-

docs/notebooks/.envrc

@@ -1 +1 @@
-use conda vitessce-python-notebooks
+use conda vitessce-python-notebooks

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

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