3.10 and 3.11 good, still problems with 3.12

Author: standage

.github/workflows/conda-test.yml

@@ -29,7 +29,7 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: setup miniconda
+    - name: setup environment with miniconda
       uses: conda-incubator/setup-miniconda@v3
       with:
         auto-update-conda: true
@@ -53,16 +53,12 @@ jobs:
     - name: install package
       run: |
         ls -lhp
-        pip install .
+        pip install .[test]
 
     - name: get plannotate dbs
       run: |
         python -c "from plannotate.resources import download_databases; download_databases()"
 
-    - name: Install pytest
-      run: |
-        conda install pytest
-
     - name: pytest
       run: |
         pytest --version

environment.yml

@@ -3,18 +3,8 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - altair=4.2.2
-  - biopython>=1.78
   - blast>=2.10.1
-  - bokeh==2.4.3
-  - click
   - curl
   - diamond>=2.0.13
-  - numpy>1,<2
-  - pandas>=1.3.5,<3.0
-  - protobuf>=3.20.3
-  - python>=3.10,<3.13
-  - ripgrep>=13.0.0
-  - streamlit>=1.22,<1.42
-  - tabulate>=0.8.9
+  - python>=3.12,<3.13
   - trnascan-se>=2.0.7

plannotate/streamlit_app.py

@@ -186,7 +186,7 @@ def setup_page():
 
     st.markdown(hide_streamlit_style, unsafe_allow_html=True)
 
-    st.image(rsc.get_image("pLannotate.png"), use_column_width="auto")
+    st.image(rsc.get_image("pLannotate.png"), use_container_width="auto")
 
     st.markdown(
         f'<div style="text-align: right; font-size: 0.9em"> {plannotate_version} </div>',

pyproject.toml

@@ -7,6 +7,23 @@ requires-python = ">=3.10,<3.13"
 authors = [
     {name = "Matt McGuffie", email = "mmcguffi@gmail.com"},
 ]
+dependencies = [
+    "altair==4.2.2",
+    "biopython>=1.78",
+    "bokeh==2.4.3",
+    "click",
+    "numpy==1.23; python_version < '3.12'",
+    "numpy>=1.26; python_version >= '3.12'",
+    "pandas>=1.3.5,<2; python_version == '3.10'",
+    "pandas>=1.3.5,<3; python_version > '3.10'",
+    "protobuf>=3.20.3",
+    "ripgrep>=13",
+    "streamlit>=1.36,<1.42",
+    "tabulate>=0.8.9",
+]
+
+[project.optional-dependencies]
+test = ["pytest", "pytest-cov"]
 
 [project.scripts]
 plannotate = "plannotate.pLannotate:main"