Merge pull request #83 from openworm/master

Use latest master for ow-0.9.5 release
openworm · Oct 28, 2024 · 448237c · 448237c
2 parents e9077b9 + 9555bc9
commit 448237c
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diff --git a/.github/workflows/non_omv.yml b/.github/workflows/non_omv.yml
@@ -14,7 +14,7 @@ jobs:
       fail-fast: false
       matrix:        
         runs-on: [ubuntu-latest, macos-12, macos-latest ]
-        python-version: [ 3.8, 3.9, "3.10" ]
+        python-version: [ 3.8, 3.9, "3.10", "3.11" ]
         exclude:
           - runs-on: macos-latest
             python-version: "3.8"
@@ -43,7 +43,9 @@ jobs:
         pip list
         
     - name: Test OpenWormReader with owmeta
+      if: ${{ matrix.python-version != '3.11' }}
       run: |
+        pip install owmeta>=0.12.3
         owm bundle remote --user add ow 'https://raw.githubusercontent.com/openworm/owmeta-bundles/master/index.json'
         python -m c302.OpenWormReader
 

diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
@@ -0,0 +1,36 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/.gitignore b/.gitignore
@@ -105,3 +105,4 @@ arm64
 /examples/test/images/c302_C1_Pharyngeal.net.nml
 /examples/test/images/c302_C1_Social.net.nml
 /examples/test/images/c302_C1_Syns.net.nml
+*ken.sh
diff --git a/README.md b/README.md
@@ -9,27 +9,33 @@ c302 is a framework for generating network models in NeuroML 2 based on *C. eleg
 
 ![c302 structure](https://raw.githubusercontent.com/openworm/CElegansNeuroML/master/CElegans/pythonScripts/c302/images/c302.png)
 
-It uses information on the synaptic connectivity of the network (from [here](https://github.com/openworm/c302/blob/master/c302/data/CElegansNeuronTables.xls)) and uses [libNeuroML](https://github.com/NeuralEnsemble/libNeuroML) to generate a network in valid NeuroML, which can be run in [jNeuroML](https://github.com/NeuroML/jNeuroML) or [pyNeuroML](https://github.com/NeuroML/pyNeuroML).
+It uses information on the synaptic connectivity of the network (from [here](https://github.com/openworm/c302/blob/master/c302/data)) and uses [libNeuroML](https://github.com/NeuralEnsemble/libNeuroML) to generate a network in valid NeuroML, which can be run in [jNeuroML](https://github.com/NeuroML/jNeuroML) or [pyNeuroML](https://github.com/NeuroML/pyNeuroML).
 
-**The c302 paper has recently been published!**
+**The c302 paper is out!**
 
 *c302: a multiscale framework for modelling the nervous system of Caenorhabditis elegans* Padraig Gleeson, David Lung, Radu Grosu, Ramin Hasani, Stephen D. Larson, [Phil. Trans. R. Soc. B 2018 373 20170379](http://rstb.royalsocietypublishing.org/content/373/1758/20170379); DOI: 10.1098/rstb.2017.0379.
 
 
 ### To install & test
 
-The full set of dependencies for c302 can be installed with the following (see also the [Travis-CI script](https://github.com/openworm/c302/blob/master/.travis.yml)):
+The full set of dependencies for c302 can be installed with the following (see also the [ci.yml](https://github.com/openworm/c302/blob/master/.github/workflows/ci.yml) and [non_omv.yml](https://github.com/openworm/c302/blob/master/.github/workflows/non_omv.yml) workflow files):
 
-    git clone https://github.com/openworm/c302.git
-    cd c302
-    pip install .
-    owm bundle remote --user add ow 'https://raw.githubusercontent.com/openworm/owmeta-bundles/master/index.json'
+```console
+git clone https://github.com/openworm/c302.git
+cd c302
+pip install .
+
+# The following can only be run on Mac and Linux. Note: c302 can be run without ownmeta fully installed
+owm bundle remote --user add ow 'https://raw.githubusercontent.com/openworm/owmeta-bundles/master/index.json'
+```
 
 This will install c302 as well as [pyNeuroML](https://github.com/NeuroML/pyNeuroML) and [owmeta](https://github.com/openworm/owmeta).
 
-To run the test.sh script, the Neuron simulator is also required, and should be installed as described [here](https://www.neuron.yale.edu/neuron/download).
+For Windows users a  virtual environment must be generated with Python 3.10 as any newer versions do not currently support owmeta.
+
+To run the test.sh script, the Neuron simulator is also required, and should be installed as described [here](https://www.neuron.yale.edu/neuron/download) (On Mac and Linux it can be installed with `pip install neuron`). 
 
-For Linux users, additional dependencies (OpenJDK 19 and Graphviz) are required to run the Usage Examples:
+For Linux users, additional dependencies (OpenJDK 19 and Graphviz) are required to run the usage examples:
 
     sudo apt-get install openjdk-19-jdk graphviz
 
@@ -81,7 +87,7 @@ Screenshots of a simulation with pyNeuroML of c302_B_Pharyngeal are shown below
 
 #### 1b) Run standard examples with Neuron
 
-The models can also be run using the Neuron simulator. This should be installed as outlined [here](https://www.neuron.yale.edu/neuron/download).
+The models can also be run using the Neuron simulator.  This should be installed as outlined [here](https://www.neuron.yale.edu/neuron/download). Note: running c302 with Neuron is not currently supported on Windows.
 
        cd examples
        pynml LEMS_c302_A_IClamp.xml -neuron   # Generate the Neuron files (Python/hoc/mod)

diff --git a/c302/CompareMain.py b/c302/CompareMain.py
@@ -1,11 +1,11 @@
-__author__ = 'Ari'
+__author__ = "Ari"
 
 from operator import itemgetter
 import xlrd
 import os
 
-def comparitor(fName1, fName2):
 
+def comparitor(fName1, fName2):
     path1 = fName1
     path2 = fName2
     dir = os.path.dirname(__file__)
@@ -28,17 +28,54 @@ def comparitor(fName1, fName2):
     # Print results. Give number of pairs that are matched, remained from unmatched files, and associated pairs.
     print("Number of matching pairs: " + str(len(matches[indexName2[0]])))
     for p in range(len(matches[indexName2[0]])):
-        print(str(matches[indexName2[0]][p])+" -> "+str(matches[indexName2[1]][p])+" ("+str(matches[indexName2[2]][p])+", "+str(matches[indexName2[3]][p])+")")
-    print("\nNumber of pairs unmatched in " + fName1 + " is: " + str(len(col1[indexName2[0]])))
+        print(
+            str(matches[indexName2[0]][p])
+            + " -> "
+            + str(matches[indexName2[1]][p])
+            + " ("
+            + str(matches[indexName2[2]][p])
+            + ", "
+            + str(matches[indexName2[3]][p])
+            + ")"
+        )
+    print(
+        "\nNumber of pairs unmatched in "
+        + fName1
+        + " is: "
+        + str(len(col1[indexName2[0]]))
+    )
     for p in range(len(col1[indexName2[0]])):
-        print(str(col1[indexName2[0]][p])+" -> "+str(col1[indexName2[1]][p])+" ("+str(col1[indexName2[2]][p])+", "+str(col1[indexName2[3]][p])+")")
-    print("\nNumber of pairs unmatched in " + fName2 + " is: " + str(len(col2[indexName1[0]])))
+        print(
+            str(col1[indexName2[0]][p])
+            + " -> "
+            + str(col1[indexName2[1]][p])
+            + " ("
+            + str(col1[indexName2[2]][p])
+            + ", "
+            + str(col1[indexName2[3]][p])
+            + ")"
+        )
+    print(
+        "\nNumber of pairs unmatched in "
+        + fName2
+        + " is: "
+        + str(len(col2[indexName1[0]]))
+    )
     for p in range(len(col2[indexName1[0]])):
-        print(str(col2[indexName1[0]][p])+" -> "+str(col2[indexName1[1]][p])+" ("+str(col2[indexName1[2]][p])+", "+str(col2[indexName1[3]][p])+")")
+        print(
+            str(col2[indexName1[0]][p])
+            + " -> "
+            + str(col2[indexName1[1]][p])
+            + " ("
+            + str(col2[indexName1[2]][p])
+            + ", "
+            + str(col2[indexName1[3]][p])
+            + ")"
+        )
 
 
 # Get columns from .txt files
-def getColumns(fileIn, delim = "\t", header = True):
+def getColumns(fileIn, delim="\t", header=True):
     cols = {}
     indexName = {}
     for lineNum, line in enumerate(fileIn):
@@ -63,6 +100,7 @@ def getColumns(fileIn, delim = "\t", header = True):
                 i += 1
     return cols, indexName
 
+
 # Get columns from .xls files
 def getColumnsXls(fileIn):
     cols = {}
@@ -92,16 +130,19 @@ def getColumnsXls(fileIn):
             cols[indexName[curr_cell]] += [cell_value]
     return cols, indexName
 
+
 # Sort dictionaries by first two column (From/To Neurons), first by one, then the other.
 def sortTwoColumns(cols):
-    cols = sorted(cols, key = itemgetter(0,1))
+    cols = sorted(cols, key=itemgetter(0, 1))
+
 
 # Formatting involved removing any filler zeros from the middle of strings.
 def formatNames(cols, indexName):
     for i in range(2):
         for char in cols[indexName[i]]:
-            if char[-1] != '0':
-                char = "".join(char.split("0",1))
+            if char[-1] != "0":
+                char = "".join(char.split("0", 1))
+
 
 # Compare two lists, create new list of matching pairs, remove pairs from respective original lists.
 def matchLists(cols1, cols2, indexName1, indexName2):
@@ -134,7 +175,9 @@ def matchLists(cols1, cols2, indexName1, indexName2):
                 if x2 == pair:
                     index2 = p2
             # If matches array does not contain current pair from long array, add it
-            if not zip(matches[indexNames1[0]], matches[indexNames1[1]]).__contains__(([pair[0]],[pair[1]])):
+            if not zip(matches[indexNames1[0]], matches[indexNames1[1]]).__contains__(
+                ([pair[0]], [pair[1]])
+            ):
                 # print(matches[indexNames1[0]], matches[indexNames1[1]])
                 for i in range(len(indexNames1)):
                     if col1[indexNames1[i]][index1] == col2[indexNames2[i]][index2]:
@@ -144,17 +187,23 @@ def matchLists(cols1, cols2, indexName1, indexName2):
                         del col2[indexNames2[i]][index2]
                         del col1[indexNames1[i]][index1]
                     else:
-                        matches[indexNames1[i]] += [[col1[indexNames1[i]][index1], col2[indexNames2[i]][index2]]]
+                        matches[indexNames1[i]] += [
+                            [col1[indexNames1[i]][index1], col2[indexNames2[i]][index2]]
+                        ]
                         del col2[indexNames2[i]][index2]
                         del col1[indexNames1[i]][index1]
             # If pair is already in array, add value from last two columns to array
             else:
-                for p3, x3 in enumerate(zip(matches[indexNames1[0]], matches[indexNames1[1]])):
+                for p3, x3 in enumerate(
+                    zip(matches[indexNames1[0]], matches[indexNames1[1]])
+                ):
                     if x3 == ([pair[0]], [pair[1]]):
                         index3 = p3
                 for i in range(len(indexNames1)):
                     if i > 1:
-                        matches[indexNames1[i]][index3] += [col1[indexNames1[i]][index1]]
+                        matches[indexNames1[i]][index3] += [
+                            col1[indexNames1[i]][index1]
+                        ]
                     del col1[indexNames1[i]][index1]
                     del col2[indexNames2[i]][index2]
 
@@ -164,8 +213,12 @@ def matchLists(cols1, cols2, indexName1, indexName2):
             if x1 == pair:
                 index1 = p1
         # If matches array does contain current pair from long array, add its conn. type and number
-        if zip(matches[indexNames1[0]], matches[indexNames1[1]]).__contains__(([pair[0]],[pair[1]])):
-            for p3, x3 in enumerate(zip(matches[indexNames1[0]], matches[indexNames1[1]])):
+        if zip(matches[indexNames1[0]], matches[indexNames1[1]]).__contains__(
+            ([pair[0]], [pair[1]])
+        ):
+            for p3, x3 in enumerate(
+                zip(matches[indexNames1[0]], matches[indexNames1[1]])
+            ):
                 if x3 == ([pair[0]], [pair[1]]):
                     index3 = p3
             for i in range(len(indexNames1)):
@@ -183,7 +236,9 @@ def matchLists(cols1, cols2, indexName1, indexName2):
         for p4, x4 in enumerate(zip(matches[indexNames1[0]], matches[indexNames1[1]])):
             if x4 == ([pair[1]], [pair[0]]):
                 index4 = p4
-        if zip(matches[indexNames1[0]], matches[indexNames1[1]]).__contains__(([pair[1]], [pair[0]])):
+        if zip(matches[indexNames1[0]], matches[indexNames1[1]]).__contains__(
+            ([pair[1]], [pair[0]])
+        ):
             # print(zip(matches[indexNames1[0]], matches[indexNames1[1]]))
             # print(([pair[1]], [pair[0]]))
             for i in range(len(indexNames1)):
@@ -193,26 +248,26 @@ def matchLists(cols1, cols2, indexName1, indexName2):
                     matches[indexNames1[i]][index4] += [col1[indexNames1[i]][index1]]
                 del col1[indexNames1[i]][index1]
 
-
     return matches, col1, col2
 
+
 # Option of additional formatting to shorten lists. Not used. Not complete.
 # 'EJ' maps to 'GapJunction'.
 # 'R', 'Rp', 'S', 'Sp' map to 'Send'.
 # 'NMJ' does not map.
 def typeMapping(cols1, cols2, indexName1, indexName2):
-    list1 = ['GapJunction','Send']
-    list2 = ['EJ','NMJ','R','Rp','S','Sp']
+    list1 = ["GapJunction", "Send"]
+    list2 = ["EJ", "NMJ", "R", "Rp", "S", "Sp"]
     type1 = cols1[indexName1[2]]
     type2 = cols2[indexName2[2]]
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     fName1 = "CElegansNeuronTables.xls"
     fName2 = "NeuronConnectFormatted.xlsx"
 
     # file1 = "C:\\Users\\Ari\\Documents\\Projects\\OpenWorm\\book1.txt"
     # file2 = "C:\\Users\\Ari\\Documents\\Projects\\OpenWorm\\book2.txt"
     # xfile1 = "C:\\Users\\Ari\\Documents\\Projects\\OpenWorm\\CElegansNeuroML\\CElegansNeuronTables.xls"
     # xfile2 = "C:\\Users\\Ari\\Documents\\Projects\\OpenWorm\\CElegansNeuroML\\NeuronConnectFormatted.xlsx"
-    comparitor(fName1,fName2)
+    comparitor(fName1, fName2)