windows fix (temporarily)

.github/workflows/run-pytest-windows.yml

@@ -0,0 +1,32 @@
+name: Run pytests windows
+
+on:
+  push:
+    branches: [dev]
+  pull_request:
+    branches: [master, dev]
+
+jobs:
+  pytest:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+        os: [windows-latest]
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install test dependencies
+      run: if [ -f requirements/requirements-test.txt ]; then pip install -r requirements/requirements-test.txt; fi
+
+    - name: Install package
+      run: python -m pip install .
+
+    - name: Run pytest tests
+      run: pytest tests -x -vv

.github/workflows/run-pytest.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.8", "3.11"]
+        python-version: ["3.8", "3.12"]
         os: [ubuntu-latest]
 
     steps:

geofetch/geofetch.py

@@ -372,10 +372,17 @@ def fetch_all(self, input: str, name: str = None) -> Union[NoReturn, peppy.Proje
         # check to make sure prefetch is callable
         if not self.just_metadata and not self.processed:
             if not is_command_callable("prefetch"):
-                raise SystemExit(
-                    "To download raw data You must first install the sratoolkit, with prefetch in your PATH."
-                    " Installation instruction: http://geofetch.databio.org/en/latest/install/"
-                )
+                if os.name == "nt":
+                    _LOGGER.warning(
+                        "GEOfetch is not checking if prefetch is installed on Windows,"
+                        " please make sure it is installed and in your PATH, otherwise "
+                        "it will not be possible to download raw data."
+                    )
+                else:
+                    raise SystemExit(
+                        "To download raw data You must first install the sratoolkit, with prefetch in your PATH."
+                        " Installation instruction: http://geofetch.databio.org/en/latest/install/"
+                    )
 
         acc_GSE_list = parse_accessions(
             input, self.metadata_expanded, self.just_metadata
@@ -1036,7 +1043,7 @@ def _write_processed_annotation(
         )
 
         if not just_object:
-            with open(file_annotation_path, "w") as m_file:
+            with open(file_annotation_path, "w", encoding="utf-8") as m_file:
                 dict_writer = csv.DictWriter(m_file, processed_metadata[0].keys())
                 dict_writer.writeheader()
                 dict_writer.writerows(processed_metadata)
@@ -1865,12 +1872,13 @@ def _get_SRA_meta(self, file_gse_content: list, gsm_metadata, file_sra=None):
             else:
                 # open existing annotation
                 _LOGGER.info("Found SRA metadata, opening..")
-                with open(file_sra, "r") as m_file:
+                with open(file_sra, "r", encoding="UTF-8") as m_file:
                     reader = csv.reader(m_file)
                     file_list = []
                     srp_list = []
                     for k in reader:
-                        file_list.append(k)
+                        if k:
+                            file_list.append(k)
                     for value_list in file_list[1:]:
                         srp_list.append(dict(zip(file_list[0], value_list)))
 

geofetch/utils.py

@@ -275,7 +275,7 @@ def fetch_metadata(
                 os.makedirs(dirpath)
 
             # save file:
-            with open(outpath, "w") as f:
+            with open(outpath, "w", encoding="utf-8") as f:
                 f.write(result_text)
 
         return result_list