Merge pull request #20 from pgleeson/main

Add hive plots

.github/workflows/ci-pages.yml

@@ -10,23 +10,41 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+
       - name: Configure Git Credentials
         run: |
           git config user.name github-actions[bot]
           git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+
       - uses: actions/setup-python@v5
         with:
           python-version: 3.x
-      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV 
 
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV 
 
       - uses: actions/cache@v4
         with:
           key: mkdocs-material-${{ env.cache_id }}
           path: .cache
           restore-keys: |
             mkdocs-material-
-      - run: |
-          pip install .[docs]
-
+  
+      - name: Install HDF5 for pytables on macos-latest
+        if: ${{ matrix.runs-on == 'macos-latest' }}
+        run: |
+          brew install hdf5
+          
+          
+      - name: Install full package
+        run: |
+          pip install .[all]
+          pip list
+          
+          
+      - name: Run test script to regenerate
+        run: |
+          ./test.sh
+          ls -alt docs/
+          ls -alt docs/assets/
+  
       - run: mkdocs gh-deploy --force

.github/workflows/non_omv.yml

@@ -39,9 +39,9 @@ jobs:
         pip list
         
         
-    - name: Run test script
+    - name: Run quick test script
       run: |
-        ./test.sh
+        ./test.sh -q
         
     - name: Final version info
       run: |

.gitignore

@@ -7,3 +7,4 @@ __pycache__
 /.DS_Store
 /cect/data/~$*
 /pdfs/*.pdf
+/cect/hive.json

cect/Cells.py

@@ -27,6 +27,9 @@
     "Serotonin_Glutamate",
 ]
 
+GENERIC_CHEM_SYN = "Generic_CS"
+GENERIC_ELEC_SYN = "Generic_GJ"
+
 EXTRASYNAPTIC_SYN_TYPE = "Extrasynaptic"
 MONOAMINERGIC_SYN_CLASS = "Monoaminergic"
 PEPTIDERGIC_SYN_CLASS = "Peptidergic"
@@ -1435,6 +1438,39 @@
 )
 
 
+def get_SIM_class(cell):
+    """
+    PROVISIONAL method to return whether a cell is Sensory/Interneuron/Motorneuron (or Other)
+
+    Parameters:
+    cell: which cell to assess
+
+    Returns:
+    str: whether a cell is Sensory/Interneuron/Motorneuron (or Other)
+    """
+
+    pharyngeal_polymodal_to_class_motor = [
+        "MI",
+        "NSML",
+        "NSMR",
+        "MCL",
+        "MCR",
+    ]
+    pharyngeal_polymodal_to_class_sensory = [
+        "NSML",
+        "NSMR",
+    ]
+
+    if cell in SENSORY_NEURONS_COOK + pharyngeal_polymodal_to_class_sensory:
+        return "Sensory"
+    elif cell in MOTORNEURONS_COOK + pharyngeal_polymodal_to_class_motor:
+        return "Motorneuron"
+    elif cell in INTERNEURONS_COOK:
+        return "Interneuron"
+    else:
+        return "Other"
+
+
 def is_bilateral_left(cell):
     if (
         cell in ALL_PREFERRED_CELL_NAMES
@@ -1701,9 +1737,9 @@ def _generate_cell_table(cell_type, cells):
     print_(" - Adding table for %s" % cell_type)
 
     syn_summaries = {
-        "Chemical conns in": ["Generic_CS"] + ALL_KNOWN_CHEMICAL_NEUROTRANSMITTERS,
-        "Chemical conns out": ["Generic_CS"] + ALL_KNOWN_CHEMICAL_NEUROTRANSMITTERS,
-        "Electrical conns": ["Generic_GJ"],
+        "Chemical conns in": [GENERIC_CHEM_SYN] + ALL_KNOWN_CHEMICAL_NEUROTRANSMITTERS,
+        "Chemical conns out": [GENERIC_CHEM_SYN] + ALL_KNOWN_CHEMICAL_NEUROTRANSMITTERS,
+        "Electrical conns": [GENERIC_ELEC_SYN],
     }
 
     fig_md = ""