Merge pull request #1247 from StochSS/develop

Release v2.4

.github/workflows/main.yml

@@ -2,7 +2,7 @@ on: [push, pull_request]
 
 jobs:
   run_tests:
-    runs-on: ubuntu-16.04
+    runs-on: ubuntu-20.04
     name: StochSS Continuous Testing
     steps:
       # Checkout

.github/workflows/pylint_on_pull_request.yml

@@ -2,7 +2,7 @@ name: PyLint On Pull Request
 on: [pull_request]
 jobs:
   build:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-20.04
     steps:
     - name: Set Up Python
       uses: actions/setup-python@v2
@@ -26,37 +26,50 @@ jobs:
       env:
         HEAD_REF: ${{ github.event.pull_request.head.ref }}
       if: always()
+    - name: Set Base Lint to 0
+      run: echo BASE_LINT=0 >> $GITHUB_ENV
+      if: env.BASE_LINT == ''
     - name: Checkout Head
       run: git checkout $HEAD_REF
       env:
         HEAD_REF: ${{ github.event.pull_request.head.ref }}
-    - name: Get Lint Delta Sign (+/-)
-      run: |
-        echo PASSING_SCORE=$(git diff --name-only --diff-filter=M $BASE_REF | grep -E "\.py" | xargs pylint | grep -Eo "10, [+-]" | grep -Eo [+-] ) >> $GITHUB_ENV
-      env:
-        BASE_REF: ${{ github.event.pull_request.base.ref }}
-      if: always()
     - name: Get Head Lint Score
       run: |
         echo HEAD_LINT=$(git diff --name-only --diff-filter=M $BASE_REF | grep -E "\.py" | xargs pylint | grep -E -o "at [0-9.-]+" | grep -E -o [0-9.-]+) >> $GITHUB_ENV
       env:
         BASE_REF: ${{ github.event.pull_request.base.ref }}
       if: always()
+    - name: Set Head Lint to 0
+      run: echo HEAD_LINT=0 >> $GITHUB_ENV
+      if: env.HEAD_LINT == ''
     - name: Get Added Files Lint Score
       run: |
         echo ADDED_LINT=$(git diff --name-only --diff-filter=A $BASE_REF | grep -E "\.py" | xargs pylint | grep -E -o "at [0-9.-]+" | grep -E -o [0-9.-]+) >> $GITHUB_ENV
       env:
         BASE_REF: ${{ github.event.pull_request.base.ref }}
       if: always()
+    - name: Get Delta
+      run: |
+        import os
+        base = float(os.environ['BASE_LINT'])
+        head = float(os.environ['HEAD_LINT'])
+        delta = head - base
+        os.popen(f"echo DELTA={round(delta, 2)} >> $GITHUB_ENV")
+      shell: python
     - name: Display Results
       run: |
         echo "Lint of modified files in base:"
         echo ${{ env.BASE_LINT }}
         echo "Lint of modified files in head:"
         echo ${{ env.HEAD_LINT }}
+        echo "Delta (+/-):"
+        echo ${{ env.DELTA }}
         echo "Lint of files added by head:"
         echo ${{ env.ADDED_LINT }}
       if: always()
     - name: Fail If Negative Delta
-      run: exit 1
-      if: env.PASSING_SCORE == '-'
+      run: |
+        import os
+        if float(os.environ['HEAD_LINT']) < 9 and float(os.environ['DELTA']) < 0:
+            raise Exception("Head lint score < 9 and negative delta.")
+      shell: python

.gitignore

@@ -11,14 +11,15 @@ stochss/dist/stochss-project-manager.html
 stochss/dist/multiple-plots-page.html
 stochss/dist/stochss-domain-editor.html
 stochss/dist/stochss-loading-page.html
-stochss/dist/stochss-project-browser.html
 stochss/dist/stochss-quick-start.html
 stochss/dist/stochss-user-home.html
 jupyterhub/templates/page.html
 jupyterhub/templates/stochss-home.html
 jupyterhub/templates/stochss-job-presentation.html
 jupyterhub/templates/stochss-model-presentation.html
 jupyterhub/templates/stochss-notebook-presentation.html
+jupyterhub/templates/multiple-plots-page.html
+
 *.swp
 *.swo
 package-lock.json

Dockerfile

@@ -21,6 +21,10 @@ COPY --chown=jovyan:users public_models/ /home/jovyan/Examples
 
 COPY --chown=jovyan:users . /stochss  
 
+COPY --chown=jovyan:users /stochss/dist/favicon.ico $JUPYTER_CONFIG_DIR/custom/favicon.ico
+
+COPY --chown=jovyan:users custom.js $JUPYTER_CONFIG_DIR/custom/custom.js
+
 COPY --chown=jovyan:users stochss-logo.png $JUPYTER_CONFIG_DIR/custom/logo.png
 
 COPY --chown=jovyan:users custom.css $JUPYTER_CONFIG_DIR/custom/custom.css

Makefile

@@ -65,15 +65,19 @@ jupyterhub/secrets/postgres.env:
 jupyterhub/userlist:
 	@echo "You're missing a userlist file. We'll make a blank one for you."
 	@echo "If you'd like to set admins to jupyterhub, add entries to the userlist file"
-	@echo "in the jupyterhub/ directory like this (one user per line):"
-	@echo "[email protected] admin"
+	@echo "	in the jupyterhub/ directory like this (one user per line):"
+	@echo "	[email protected] admin"
+	@echo "If you'd like to set power users who are exempt from resource constraints"
+	@echo "	use entries like this:"
+	@echo "	[email protected] power"
+	@echo ""
 	@touch $@
 
 check-files: jupyterhub/userlist jupyterhub/secrets/.oauth.dummy.env jupyterhub/secrets/postgres.env
 
 check_files_staging: check-files jupyterhub/secrets/.oauth.staging.env
 
-check_files_prod: check-files jupyterhub/secrets/.oauth.prod.env
+check_files_prod: check-files jupyterhub/secrets/.oauth.prod.env jupyterhub/.power_users
 
 cert:
 	@echo "Generating certificate..."
@@ -126,37 +130,37 @@ hub: build_hub build run_hub_dev
 build_clean:
 	docker build \
 		--build-arg JUPYTER_CONFIG_DIR=$(JUPYTER_CONFIG_DIR) \
-	 	--no-cache -t $(DOCKER_STOCHSS_IMAGE):latest .
+		--no-cache -t $(DOCKER_STOCHSS_IMAGE):latest .
 
 create_working_dir:
 	$(DOCKER_SETUP_COMMAND)
 
-build:  
+build:
 	docker build \
 		--build-arg JUPYTER_CONFIG_DIR=$(JUPYTER_CONFIG_DIR) \
-	  	-t $(DOCKER_STOCHSS_IMAGE):latest .
+		-t $(DOCKER_STOCHSS_IMAGE):latest .
 
-test:   create_working_dir
+test: create_working_dir
 	docker run --rm \
 		--name $(DOCKER_STOCHSS_IMAGE) \
 		--env-file .env \
 		-v $(DOCKER_ROOT_DIR):/stochss \
 		-v $(DOCKER_WORKING_DIR):/home/jovyan/ \
 		-p 8888:8888 \
 		$(DOCKER_STOCHSS_IMAGE):latest \
-                /stochss/stochss/tests/run_tests.py
+		/stochss/stochss/tests/run_tests.py
 
 build_and_test: build test
 
-run:    create_working_dir
+run: create_working_dir
 	$(PYTHON_EXE) launch_webbrowser.py &
 	docker run --rm \
 		--name $(DOCKER_STOCHSS_IMAGE) \
 		--env-file .env \
 		-v $(DOCKER_WORKING_DIR):/home/jovyan/ \
 		-p 8888:8888 \
 		$(DOCKER_STOCHSS_IMAGE):latest \
-		bash -c "cd /home/jovyan;  start-notebook.sh "
+		bash -c "cd /home/jovyan; start-notebook.sh "
 
 
 build_and_run: build run

README.md

@@ -59,7 +59,7 @@ StochSS uses [JupyterHub](https://jupyterhub.readthedocs.io/en/stable/#) as the
 
 - [Optional] To set admins for JupyterHub, make a file called `userlist` in the `jupyterhub/` directory. On each line of this file place a username followed by the word 'admin'. For example: `myuser admin`. If using Google OAuth, the uesername will be a Gmail address. Navigate to `/hub/admin` to use the JupyterHub admin interface.
 
-- [Optional] By default multi-user StochSS is set up to allocate 2 logical cpus per user, reserving 2 logical cpus for the hub container and underlying OS. You can define a list of "power users" that are excluded from resource limitations by adding a text file called `.power_users` (note the leading period) to the `jupyterhub/` directory with one username/email address on each line of the file.
+- [Optional] By default multi-user StochSS is set up to allocate 2 logical cpus per user, reserving 2 logical cpus for the hub container and underlying OS. You can define "power users" that are excluded from resource limitations using the same method as above for adding an admin, but instead of following the username with 'admin', use the keyword 'power' instead.
 
 ### Run Locally
 

__version__.py

@@ -5,7 +5,7 @@
 # @website https://github.com/stochss/stochss
 # =============================================================================
 
-__version__ = '2.3.12'
+__version__ = '2.4'
 __title__ = 'StochSS'
 __description__ = 'StochSS is an integrated development environment (IDE) \
                     for simulation of biochemical networks.'

client/app.js

@@ -132,21 +132,21 @@ let getBrowser = () => {
   return {"name":BrowserDetect.browser,"version":BrowserDetect.version};
 }
 
-let validateName = (input, rename = false) => {
-  var error = ""
+let validateName = (input, {rename=false, saveAs=true}={}) => {
+  var error = "";
   if(input.endsWith('/')) {
-    error = 'forward'
+    error = 'forward';
   }
-  var invalidChars = "`~!@#$%^&*=+[{]}\"|:;'<,>?\\"
-  if(rename) {
-    invalidChars += "/"
+  var invalidChars = "`~!@#$%^&*=+[{]}\"|:;'<,>?\\";
+  if(rename || !saveAs) {
+    invalidChars += "/";
   }
   for(var i = 0; i < input.length; i++) {
     if(invalidChars.includes(input.charAt(i))) {
-      error = error === "" || error === "special" ? "special" : "both"
+      error = error === "" || error === "special" ? "special" : "both";
     }
   }
-  return error
+  return error;
 }
 
 let newWorkflow = (parent, mdlPath, isSpatial, type) => {
@@ -157,7 +157,7 @@ let newWorkflow = (parent, mdlPath, isSpatial, type) => {
   let ext = isSpatial ? /.smdl/g : /.mdl/g
   let typeCode = type === "Ensemble Simulation" ? "_ES" : "_PS";
   let name = mdlPath.split('/').pop().replace(ext, typeCode)
-  let modal = $(modals.newWorkflowHtml(name, type)).modal();
+  let modal = $(modals.createWorkflowHtml(name, type)).modal();
   let okBtn = document.querySelector('#newWorkflowModal .ok-model-btn');
   let input = document.querySelector('#newWorkflowModal #workflowNameInput');
   okBtn.disabled = false;
@@ -213,12 +213,22 @@ documentSetup = () => {
 }
 
 copyToClipboard = (text, success, error) => {
+  fullURL = window.location.protocol + '//' + window.location.hostname + text;
   if (window.clipboardData && window.clipboardData.setData) {
     // Internet Explorer-specific code path to prevent textarea being shown while dialog is visible.
-    return window.clipboardData.setData("Text", text);
+    return window.clipboardData.setData("Text", fullURL);
   }
   else {
-    navigator.clipboard.writeText(text).then(success, error)
+    navigator.clipboard.writeText(fullURL).then(success, error)
+  }
+}
+
+let switchToEditTab = (view, section) => {
+  let elementID = Boolean(view.model && view.model.elementID) ? view.model.elementID + "-" : "";
+  if($(view.queryByHook(elementID + 'view-' + section)).hasClass('active')) {
+    $(view.queryByHook(elementID + section + '-edit-tab')).tab('show');
+    $(view.queryByHook(elementID + 'edit-' + section)).addClass('active');
+    $(view.queryByHook(elementID + 'view-' + section)).removeClass('active');
   }
 }
 
@@ -234,7 +244,9 @@ module.exports = {
     postXHR: postXHR,
     tooltipSetup: tooltipSetup,
     documentSetup: documentSetup,
-    copyToClipboard: copyToClipboard
+    copyToClipboard: copyToClipboard,
+    switchToEditTab: switchToEditTab,
+    validateName: validateName
 };