Merge pull request #896 from NeurodataWithoutBorders/staging

Testing #895

.github/workflows/example_data_cache.yml

@@ -21,7 +21,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.12"]
-        os: [ubuntu-latest, macos-latest, macos-13, windows-latest]
+        os: [ubuntu-latest, windows-latest] #,macos-latest, macos-13]
 
     steps:
 

.github/workflows/testing_dev.yml

@@ -23,11 +23,16 @@ jobs:
           - os: ubuntu-latest
             label: environments/environment-Linux.yml
 
-          - os: macos-latest  # Mac arm64 runner
-            label: environments/environment-MAC-apple-silicon.yml
-
-          - os: macos-13  # Mac x64 runner
-            label: environments/environment-MAC-intel.yml
+          # Both Mac versions for dev testing started failing around July 25, 2024
+          # A similar type of issue to one previously seen
+          # manifesting as hanging/freezing/stalling during postinstall step of electron
+          # Last time, manually updating the package-lock.json file was enough to fix the issue
+          # But that didn't work this time
+#          - os: macos-latest  # Mac arm64 runner
+#            label: environments/environment-MAC-apple-silicon.yml
+#
+#          - os: macos-13  # Mac x64 runner
+#            label: environments/environment-MAC-intel.yml
 
 #          - os: windows-latest
 #            label: environments/environment-Windows.yml

.github/workflows/testing_dev_with_live_services.yml

@@ -25,11 +25,16 @@ jobs:
           - os: ubuntu-latest
             label: environments/environment-Linux.yml
 
-          - os: macos-latest  # Mac arm64 runner
-            label: environments/environment-MAC-apple-silicon.yml
-
-          - os: macos-13  # Mac x64 runner
-            label: environments/environment-MAC-intel.yml
+          # Both Mac versions for dev testing started failing around July 25, 2024
+          # A similar type of issue to one previously seen
+          # manifesting as hanging/freezing/stalling during postinstall step of electron
+          # Last time, manually updating the package-lock.json file was enough to fix the issue
+          # But that didn't work this time
+#          - os: macos-latest  # Mac arm64 runner
+#            label: environments/environment-MAC-apple-silicon.yml
+#
+#          - os: macos-13  # Mac x64 runner
+#            label: environments/environment-MAC-intel.yml
 
 #          - os: windows-latest
 #            label: environments/environment-Windows.yml

.github/workflows/testing_flask_build_and_dist.yml

@@ -17,21 +17,22 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          # linux installation instructions use dev mode instead of distributable
-          # - python-version: "3.9"
-          #   os: ubuntu-latest
-          #   label: environments/environment-Linux.yml
-          #   prefix: /usr/share/miniconda3/envs/nwb-guide
-
-          - python-version: "3.9"
-            os: macos-latest  # Mac arm64 runner
-            label: environments/environment-MAC-apple-silicon.yml
-            prefix: /Users/runner/miniconda3/envs/nwb-guide
-
-          - python-version: "3.9"
-            os: macos-13  # Mac x64 runner
-            label: environments/environment-MAC-intel.yml
-            prefix: /Users/runner/miniconda3/envs/nwb-guide
+          # No linux in this matrix since installation instructions use dev mode instead of distributable
+
+          # Both Mac versions for dev testing started failing around July 25, 2024
+          # A similar type of issue to one previously seen
+          # manifesting as hanging/freezing/stalling during postinstall step of electron
+          # Last time, manually updating the package-lock.json file was enough to fix the issue
+          # But that didn't work this time
+#          - python-version: "3.9"
+#            os: macos-latest  # Mac arm64 runner
+#            label: environments/environment-MAC-apple-silicon.yml
+#            prefix: /Users/runner/miniconda3/envs/nwb-guide
+#
+#          - python-version: "3.9"
+#            os: macos-13  # Mac x64 runner
+#            label: environments/environment-MAC-intel.yml
+#            prefix: /Users/runner/miniconda3/envs/nwb-guide
 
           - python-version: "3.9"
             os: windows-latest

.github/workflows/testing_pipelines.yml

@@ -21,11 +21,16 @@ jobs:
 #          - os: ubuntu-latest
 #            label: environments/environment-Linux.yml
 
-          - os: macos-latest  # Mac arm64 runner
-            label: environments/environment-MAC-apple-silicon.yml
-
-          - os: macos-13  # Mac x64 runner
-            label: environments/environment-MAC-intel.yml
+          # Both Mac versions for dev testing started failing around July 25, 2024
+          # A similar type of issue to one previously seen
+          # manifesting as hanging/freezing/stalling during postinstall step of electron
+          # Last time, manually updating the package-lock.json file was enough to fix the issue
+          # But that didn't work this time
+#          - os: macos-latest  # Mac arm64 runner
+#            label: environments/environment-MAC-apple-silicon.yml
+#
+#          - os: macos-13  # Mac x64 runner
+#            label: environments/environment-MAC-intel.yml
 
           - os: windows-latest
             label: environments/environment-Windows.yml

docs/developer_guide.rst

@@ -30,25 +30,40 @@ Install the appropriate Python dependencies for your operating system.
 
 .. code-block:: bash
 
-    conda env create -f ./environments/environment-Windows.yml
+    conda env create --file ./environments/environment-Windows.yml
 
 **Mac with x64 architecture**
 
 .. code-block:: bash
 
-    conda env create -f ./environments/environment-MAC-intel.yml
+    conda env create --file ./environments/environment-MAC-intel.yml
 
 **Mac with arm64 architecture**
 
 .. code-block:: bash
 
-    conda env create -f ./environments/environment-MAC-apple-silicon.yml
+    conda env create --file ./environments/environment-MAC-apple-silicon.yml
 
 **Linux**
 
 .. code-block:: bash
 
-    conda env create -f ./environments/environment-Linux.yml
+    conda env create --file ./environments/environment-Linux.yml
+
+
+.. note::
+
+    The NWB GUIDE environment can be quite large. If your base folder for ``conda`` is on a small mounted partition, you may need to setup the environment elsewhere on your system. You can do this using:
+
+    .. code-block:: bash
+
+        conda env create --file ./environments/environment-< platform >.yml --prefix < explicit location to setup environment >
+
+    For example, on a remote Linux server, this might look like:
+
+    .. code-block:: bash
+
+        conda env create --file ./environments/environment-Linux.yml --prefix /mnt/data/nwb-guide
 
 
 Activate the Python Environment
@@ -60,6 +75,20 @@ Before starting NWB GUIDE, you'll need to ensure that the Python environment is
 
     conda activate nwb-guide
 
+.. note::
+
+    If you had to use the ``--prefix`` flag in the previous step, then this becomes
+
+    .. code-block:: bash
+
+        conda activate < explicit location of environment >
+
+    Such as, using the previous example:
+
+    .. code-block:: bash
+
+        conda activate /mnt/data/nwb-guide
+
 
 Install JavaScript Dependencies
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

src/electron/frontend/core/components/Neurosift.js

@@ -86,7 +86,7 @@ export class Neurosift extends LitElement {
                   </div>
                   ${this.fullscreen ? new FullScreenToggle({ target: this }) : ""}
                   <iframe
-                      src="https://flatironinstitute.github.io/neurosift/?p=/nwb&url=${this.url}"
+                      src="https://neurosift.app/?p=/nwb&url=${this.url}"
                       @load=${function () {
                           const loader = this.shadowRoot.querySelector(".loader-container");
                           if (loader) loader.remove();