Merge branch 'master' into kotsalos/python_models

Author: alexsavulescu

.github/workflows/nrn-modeldb-ci.yaml

@@ -8,6 +8,29 @@ on:
   schedule:
     # Run at 2am every day
     - cron:  '0 2 * * *'
+  workflow_call:
+   inputs:
+      neuron_v1:
+        description: Last official release (neuron) / NEURON pinned version / Azure drop (artifacts) url
+        default: 'neuron'
+        required: true
+        type: string
+      neuron_v2:
+        description: Last nightly release (neuron-nightly) / NEURON pinned version / Azure drop (artifacts) url
+        default: 'neuron-nightly'
+        required: true
+        type: string
+      models_to_run:
+        description: 'Empty for all models, space separated accession numbers for specific models'
+        default: ''
+        required: false
+        type: string
+      repo:
+        default: 'neuronsimulator/nrn-modeldb-ci'
+        type: string
+        required: false
+      
+        
   workflow_dispatch:
     inputs:
       neuron_v1:
@@ -26,25 +49,25 @@ on:
 jobs:
   nrn-modeldb-ci:
     runs-on: ubuntu-latest
-    timeout-minutes: 60
     strategy:
       fail-fast: false
-      matrix:
-        python-version: ["3.9"]
     env:
       DISPLAY: ${{ ':0' }}
-      NEURON_V1: ${{ github.event.inputs.neuron_v1 || 'neuron' }}
-      NEURON_V2: ${{ github.event.inputs.neuron_v2 || 'neuron-nightly' }}
-      MODELS_TO_RUN: ${{ github.event.inputs.models_to_run || '' }}
+      NEURON_V1: ${{ github.event.inputs.neuron_v1 || inputs.neuron_v1 || 'neuron' }}
+      NEURON_V2: ${{ github.event.inputs.neuron_v2 || inputs.neuron_v2 || 'neuron-nightly' }}
+      MODELS_TO_RUN: ${{ github.event.inputs.models_to_run || inputs.models_to_run || '' }}
 
     steps:
-    - uses: actions/checkout@v2
 
-    - name: check for Azure drop NEURON_V1 -> ${{ github.event.inputs.neuron_v1 }}
-      if: github.event_name == 'workflow_dispatch' && startsWith(github.event.inputs.neuron_v1, 'https://dev.azure.com/neuronsimulator/')
+    - uses: actions/checkout@v3
+      with:
+        repository: ${{ inputs.repo || github.repository }}
+        
+    - name: check for Azure drop NEURON_V1 -> ${{ env.NEURON_V1 }}
+      if: startsWith(env.NEURON_V1, 'https://dev.azure.com/neuronsimulator/')
       run: |
         # check URI
-        curl -sfSI -X GET '${{ github.event.inputs.neuron_v1 }}'
+        curl -sfSI -X GET '${{ env.NEURON_V1 }}'
         
         # Download Azure drop and unzip
         AZURE_DROP_URL="$NEURON_V1"
@@ -56,11 +79,11 @@ jobs:
         # Set drop dir in the env
         echo "DROP_DIR_V1=`pwd`/DROP_V1" >> $GITHUB_ENV
     
-    - name: check for Azure drop NEURON_V2 -> ${{ github.event.inputs.neuron_v2 }}
-      if: github.event_name == 'workflow_dispatch' && startsWith(github.event.inputs.neuron_v2, 'https://dev.azure.com/neuronsimulator/')
+    - name: check for Azure drop NEURON_V2 -> ${{ env.NEURON_V2 }}
+      if: startsWith(env.NEURON_V2, 'https://dev.azure.com/neuronsimulator/')
       run: |
         # check URI
-        curl -sfSI -X GET '${{ github.event.inputs.neuron_v2 }}'
+        curl -sfSI -X GET '${{ env.NEURON_V2 }}'
 
         # Download Azure drop and unzip
         AZURE_DROP_URL="$NEURON_V2"
@@ -72,25 +95,36 @@ jobs:
         # Set drop dir in the env
         echo "DROP_DIR_V2=`pwd`/DROP_V2" >> $GITHUB_ENV
 
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+    - uses: actions/setup-python@v4
       with:
-        python-version: ${{ matrix.python-version }}
-
+        python-version: 3.9
+        
     - name: Set models to run for PR
       run: |
-        # Select a few models to run CI for PRs 
+        # For PRs we only have a few models for quick sanity checking.
+        # Once the PR is green you need to manually run the ModelDB CI workflow by simply selecting your branch in the UI.
+
+        # The follwing selection aims to target different features (since we haven't worked on unit testing yet -> #38 ).
+        # Select a few models to run CI for PRs:
+        #   64195   -> run: null
+        #   22203   -> skip: true
+        #   156120  -> several model directories
+        #   97868   -> failed nrnivmodl
+        #   146030  -> curate_patterns
+        #   244679  -> no entry in modeldb-run.yaml
+        #   rest:   -> currently yielding differences in the pipeline
+        #echo 'MODELS_TO_RUN=64195 22203 156120 51781 97868 22203 97756 97917 105507 136803 138379 138382 146030 244679 251881' >> $GITHUB_ENV
         #TODO - temporary run added python models
         echo 'MODELS_TO_RUN=156039 194897 226422 186768 189922 195615 139421 144586 244412 39948 195569 249404 206400 144511 229276 151282 264834 151685' >> $GITHUB_ENV
-      if: github.event_name == 'pull_request'
+      if: github.event_name == 'pull_request' && inputs.repo == ''
 
     - name: Install dependencies and project
       id: install-deps
       run: |
         set
         # Set up Xvfb
         sudo apt-get install xvfb
-        sudo /usr/bin/Xvfb $DISPLAY -screen 0 1600x1200x24 &  # run in bg
+        sudo /usr/bin/Xvfb $DISPLAY -screen 0 1600x1200x24 -noreset -nolock -shmem &  # run in bg
         # Install python dependencies
         python -m pip install --upgrade pip
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
@@ -155,7 +189,7 @@ jobs:
       run: |
         diffreports2html ${nrn1_ver}.json ${nrn2_ver}.json
 
-    - uses: actions/upload-artifact@v2
+    - uses: actions/upload-artifact@v3
       with:
         name: ${{ env.nrn1_ver }}-vs-${{ env.nrn2_ver }}
         path: |

.github/workflows/python-publish.yml

@@ -15,7 +15,7 @@ jobs:
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
     - name: Install dependencies

README.md

@@ -224,6 +224,24 @@ Every `runmodels` report will hold out run statistics in the `"0"` key:
     },
 ```
 
+For every model there is a `<model.id>.yaml` that is dumped in the model run directory.
+This is used in case the model is re-run in `--inplace` mode (also useful for debugging). 
+
+```bash
+(venv) nrn-modeldb-ci$ cat test3682/synmap/3682.yaml
+```
+```yaml
+driver: /home/savulesc/Workspace/nrn-modeldb-ci/test3682/synmap/driver.hoc
+init: /home/savulesc/Workspace/nrn-modeldb-ci/test3682/synmap/mosinit.hoc
+model_dir: /home/savulesc/Workspace/nrn-modeldb-ci/test3682/synmap
+script:
+- echo 'use_mcell_ran4(1)' > temp
+- cat mosinit.hoc >> temp
+- mv temp  mosinit.hoc
+start_dir: /home/savulesc/Workspace/nrn-modeldb-ci/test3682/synmap
+(venv) savulesc@bbd-cjngk03:~/Workspace/nrn-modeldb-ci$ 
+```
+
 ## Funding
 
 

modeldb/commands.py

@@ -36,6 +36,7 @@ def runmodels(args=None):
         --virtual               Run in headless mode. You need a back-end like Xvfb.
         --clean                 Auto-clean model working directory before running (useful for consecutive runs and failsafe)
         --norun                 Compile and link only (nrnivmodl).
+        --inplace               Skip model preparation logic, simply run NEURON.
 
     Examples
         runmodels --workdir=/path/to/workdir                        # run all models
@@ -48,22 +49,29 @@ def runmodels(args=None):
     virtual = options.pop("--virtual", False)
     clean = options.pop("--clean", False)
     norun = options.pop("--norun", False)
+    inplace = options.pop("--inplace", False)
 
     if os.path.abspath(working_dir) == ROOT_DIR:
         print("Cannot run models directly into nrn-modeldb-ci ROOT_DIR -> {}".format(ROOT_DIR))
         sys.exit(1)
 
-    if not clean and is_dir_non_empty(working_dir):
-        print("WARNING: WorkingDirectory {} exists and is non empty.".format(working_dir))
-        print("\tre-run with --clean if you wish to overwrite model runs!")
+    if clean and inplace:
+        print("ERROR: --clean and --inplace are mutually exclusive")
         sys.exit(1)
 
-    mrm = ModelRunManager(working_dir, gout=gout, clean=clean, norun=norun)
+    if not (clean or inplace) and is_dir_non_empty(working_dir):
+        print("ERROR: WorkingDirectory {} exists and is non empty.".format(working_dir))
+        print("\t re-run with one of these options:\n"
+              "\t\t--clean \t-> if you wish to OVERWRITE model runs (delete content from --workdir and re-build from cache)\n"
+              "\t\t--inplace \t-> if you wish to re-run the same model (content in --workdir is kept)\n")
+        sys.exit(1)
+
+    mrm = ModelRunManager(working_dir, gout=gout, clean=clean, norun=norun, inplace=inplace)
     model_list = model_ids if model_ids else None
 
     if virtual:
         from pyvirtualdisplay import Display
-        with Display() as _:
+        with Display(manage_global_env=False) as _:
             mrm.run_models(model_list)
     else:
         mrm.run_models(model_list)
@@ -206,11 +214,14 @@ def diffreports2html(args=None):
     file_loader = FileSystemLoader(os.path.join(Path(__file__).parent.resolve(), 'templates'))
     env = Environment(loader=file_loader)
     template = env.get_template('diffreport.html')
+    runtime_template = env.get_template('runtimes.html')
 
     report_title = '{}-vs-{}'.format(os.path.splitext(json_report1)[0],
                                      os.path.splitext(json_report2)[0])
     report_filename = os.path.join(Path(json_report1).resolve().parent, report_title + '.html')
-    diff_dict, gout_dict = diff_reports(json_report1, json_report2)
+    runtime_report_title = 'Runtimes ' + report_title
+    runtime_report_filename = os.path.join(Path(json_report1).resolve().parent, "runtimes-" + report_title + '.html')
+    diff_dict, gout_dict,runtime_dict, v1, v2 = diff_reports(json_report1, json_report2)
 
     print('Writing {} ...'.format(report_filename))
     with open(report_filename, 'w') as fh:
@@ -220,3 +231,13 @@ def diffreports2html(args=None):
             gout_dict=gout_dict),
         )
     print('Done.')
+    print('Writing {} ...'.format(runtime_report_filename))
+    with open(runtime_report_filename, 'w') as fh:
+        fh.write(runtime_template.render(
+            title="{}".format(runtime_report_title),
+            runtime_dict=runtime_dict,
+            stats={"stats":diff_dict['0']},
+            v1=v1,
+            v2=v2),
+    )
+    print('Done.')

modeldb/modeldb-run.yaml

@@ -465,10 +465,7 @@
     - load_file("sample.hoc")
     - verify_graph_()
     script:
-    - sed 's,tstop *=,tstop = 100//,
-    - /whichAP/,$d
-    - ''' sample.hoc > temp.tmp'
-    - mv temp.tmp sample.hoc
+    -  sed -i'.bak' -e 's/tstop *=/tstop = 100\/\//g;/whichAP/,$d' sample.hoc
 76879:
     run:
     - tstop=20
@@ -503,10 +500,7 @@
 83590:
     run: []
     script:
-    - sed 's/mustart  = -0.400/mustart  = 0.800/
-    - ' s/sigmastart  = 0.064/sigmastart  = 0.128/'
-    - ''' mylibs/TFparams.hoc > temp.tmp'
-    - mv temp.tmp  mylibs/TFparams.hoc
+    - sed -i'.bak' -e 's/mustart  = -0.400/mustart  = 0.800/g;s/sigmastart  = 0.064/sigmastart  = 0.128/g' mylibs/TFparams.hoc
 84589:
     run:
     - //ignore sim in subdirectory
@@ -673,9 +667,7 @@
     - load_file("batch_.hoc")
     - verify_graph_()
     script:
-    - sed 's/batch_flag=0/batch_flag=1/
-    - s/tstop = 1e3/tstop = 20/' batch_.hoc > temp.tmp
-    - mv temp.tmp batch_.hoc
+    - sed -i'.bak' -e 's/batch_flag=0/batch_flag=1/g;s/tstop = 1e3/tstop = 20/g' batch_.hoc
 106551:
     run:
     - use_mcell_ran4(1)
@@ -823,8 +815,7 @@
     - //load_file("init.hoc")
     - //verify_graph_()
     script:
-    - sed 's/tstop = 100/tstop = 20/' init.hoc > temp.tmp
-    - mv temp.tmp init.hoc
+    - sed -i'.bak' -e 's/tstop = 100/tstop = 20/g' init.hoc
 116835:
     run:
     - tstop=10
@@ -836,8 +827,7 @@
     - run()
     - verify_graph_()
     script:
-    - sed 's/^showdemo=1/showdemo=0/' mosinit.hoc > temp.tmp
-    - mv temp.tmp mosinit.hoc
+    - sed -i'.bak' -e 's/^showdemo=1/showdemo=0/g' mosinit.hoc
 116956:
     run:
     - run()
@@ -962,16 +952,14 @@
     - run()
     - verify_graph_()
     script:
-    - sed 's/tstop = 6500/tstop = 100/' session.ses > temp.tmp
-    - mv temp.tmp session.ses
+    - sed -i'.bak' -e 's/tstop = 6500/tstop = 100/g' session.ses
 124291:
     run:
     - stim.amp = 0.1
     - runa()
     - verify_graph_()
     script: # todo -> fix model for NEURON 8.0.0 and remove this script
-    - sed 's/return 0;//' MOPP_Fig_1B_left/ichan2.mod > temp.tmp
-    - mv temp.tmp MOPP_Fig_1B_left/ichan2.mod
+    - sed -i'.bak' -e 's/return 0;//g' MOPP_Fig_1B_left/ichan2.mod
 138321:
     run:
     - run()
@@ -1076,21 +1064,21 @@
     - run()
     - verify_graph_()
     script:
-    - sed -i 's/tstop = /tstop = 50\/\//' Fig8_tuft_NMDA_spike.hoc
-    - sed -i 's/simul_iter=/simul_iter=2 \/\//' Fig8_tuft_NMDA_spike.hoc
+    - sed -i'.bak' -e 's/tstop = /tstop = 50\/\//' Fig8_tuft_NMDA_spike.hoc
+    - sed -i'.bak' -e 's/simul_iter=/simul_iter=2 \/\//' Fig8_tuft_NMDA_spike.hoc
     comment: usual simulation time is ~ 10 minutes (tstop = 120 and simul_iter=10)
 206267:
     run:
     - run()
     - verify_graph_()
     script:
-    - sed -i 's/tstop=/tstop=100 \/\//' Start.hoc
+    - sed -i'.bak' -e 's/tstop=/tstop=100 \/\//' Start.hoc
 157157:
     run:
     - run()
     - verify_graph_()
     script:
-    - sed -i 's/tstop = 5000/tstop = 250 \/\//g' PC.ses
+    - sed -i'.bak' -e 's/tstop = 5000/tstop = 250 \/\//g' PC.ses
 244848:
     run: null
     comment: not straightforward to cut down simulation time, takes too long
@@ -1105,15 +1093,20 @@
     - run()
     - verify_graph_()
     script:
-    - sed -i 's/500/5/g' BPF.hoc
-    - sed -i 's/2\([0|1]\)000/2\1/g' BPF.hoc
+    - sed -i'.bak' -e 's/500/5/g' BPF.hoc
+    - sed -i'.bak' -e 's/2\([0|1]\)000/2\1/g' BPF.hoc
     comment: diving some numbers with 100 halvened the sim time
 151126:
     run:
     - run()
     - verify_graph_()
     script:
-    - sed -i 's/tstop = 550/tstop = 100/' HAM_SR1.ses
+    - sed -i'.bak' -e 's/tstop = 550/tstop = 100/' HAM_SR1.ses
+136803:
+    run:
+    - run()
+    - verify_graph_()
+    model_dir: mod_files
 # python models
 # find * -name mosinit.py
 156039: