Add black, isort, and mypy to github tests

scientific_metadata.py is excluded from mypy temporarily.

.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}

pyproject.toml

@@ -81,4 +81,8 @@ profile = "black"
 
 [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/hdf5/scientific_metadata.py"

pyscicat/client.py

@@ -5,6 +5,7 @@
 import logging
 from datetime import datetime
 from typing import Optional
+from pathlib import Path
 from urllib.parse import quote_plus, urljoin
 
 import requests
@@ -777,13 +778,13 @@ def datasets_delete(self, pid: str) -> Optional[dict]:
     delete_dataset = datasets_delete
 
 
-def get_file_size(pathobj):
+def get_file_size(pathobj: Path):
     filesize = pathobj.lstat().st_size
     return filesize
 
 
-def get_checksum(pathobj):
-    with open(pathobj) as file_to_check:
+def get_checksum(pathobj: Path):
+    with open(pathobj,'rb') as file_to_check:
         # pipe contents of the file through
         return hashlib.md5(file_to_check.read()).hexdigest()
 
@@ -798,7 +799,7 @@ def encode_thumbnail(filename, imType="jpg"):
     return header + dataStr
 
 
-def get_file_mod_time(pathobj):
+def get_file_mod_time(pathobj: Path):
     # may only work on WindowsPath objects...
     # timestamp = pathobj.lstat().st_mtime
     return str(datetime.fromtimestamp(pathobj.lstat().st_mtime))