Merge pull request #57 from sbliven/typing-fixes

Check typing with mypy

.github/workflows/testing.yml

@@ -43,6 +43,18 @@ jobs:
       run: |
         set -vxeuo pipefail
         python -m flake8
+    
+    - name: Lint with black
+      shell: bash -l {0}
+      run: black --check .
+
+    - name: Lint with isort
+      shell: bash -l {0}
+      run: isort --check .
+
+    - name: Lint with mypy
+      shell: bash -l {0}
+      run: mypy --check pyscicat
 
     - name: Test with pytest
       shell: bash -l {0}

examples/ingest_dataset.py

@@ -1,7 +1,7 @@
 from datetime import datetime
 from pathlib import Path
 
-from pyscicat.client import encode_thumbnail, ScicatClient
+from pyscicat.client import ScicatClient, encode_thumbnail
 from pyscicat.model import Attachment, Datablock, DataFile, Dataset, Ownable
 
 # Create a client object. The account used should have the ingestor role in SciCat
@@ -31,7 +31,7 @@
     sourceFolder="/foo/bar",
     scientificMetadata={"a": "field"},
     sampleId="gargleblaster",
-    **ownable.dict()
+    **ownable.dict(),
 )
 dataset_id = scicat.upload_raw_dataset(dataset)
 
@@ -47,6 +47,6 @@
     datasetId=dataset_id,
     thumbnail=encode_thumbnail(thumb_path),
     caption="scattering image",
-    **ownable.dict()
+    **ownable.dict(),
 )
 scicat.upload_attachment(attachment)

examples/ingestion_simulation_dataset_ess.py

@@ -18,10 +18,10 @@
 
 # libraries
 import json
+
 import pyscicat.client as pyScClient
 import pyscicat.model as pyScModel
 
-
 # scicat configuration file
 # includes scicat instance URL
 # scicat user and password
@@ -68,7 +68,7 @@
         pyScModel.DataFile(**file)
         for file in dataset_information["orig_datablock"]["dataFileList"]
     ],
-    **ownable.dict()
+    **ownable.dict(),
 )
 
 # create origDatablock associated with dataset in SciCat

pyproject.toml

@@ -41,6 +41,9 @@ dev = [
     "twine",
     "black",
     "requests_mock",
+    "isort",
+    "mypy",
+    "types-requests",
 ]
 docs = [
     "ipython",
@@ -56,25 +59,16 @@ docs = [
 
 [tool.black]
 include = '\.pyi?$'
-exclude = '''
-/(
-    \.git
-  | \.hg
-  | \.mypy_cache
-  | \.tox
-  | \.venv
-  | _build
-  | buck-out
-  | build
-  | dist
-
-  # The following are specific to Black, you probably don't want those.
-  | blib2to3
-  | tests/data
-)/
-'''
+extend_exclude = 'pyscicat/_version.py'
 
+[tool.isort]
+profile = "black"
+skip_glob = ["__pycache__", "pyscicat/_version.py"]
 
 [tool.hatch]
 version.source = "vcs"
-build.hooks.vcs.version-file = "pyscicat/_version.py"
+build.hooks.vcs.version-file = "pyscicat/_version.py"
+
+[tool.mypy]
+# TODO Add type annotations and include this file
+exclude = ["pyscicat/_version.py", "pyscicat/hdf5/scientific_metadata.py"]