From d9c524b6a1e6461db885c950a125875bbc15d100 Mon Sep 17 00:00:00 2001
From: Jeremy Magland <magland@users.noreply.github.com>
Date: Thu, 25 Jul 2024 08:17:43 -0400
Subject: [PATCH 01/10] Update Neurosift URL

---
 src/electron/frontend/core/components/Neurosift.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/electron/frontend/core/components/Neurosift.js b/src/electron/frontend/core/components/Neurosift.js
index 438107205..381e6dbca 100644
--- a/src/electron/frontend/core/components/Neurosift.js
+++ b/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();

From 40f46d681001a3a0306c4e2d8f627eeac1d82584 Mon Sep 17 00:00:00 2001
From: codycbakerphd <cbaker9@nd.edu>
Date: Thu, 25 Jul 2024 10:58:57 -0400
Subject: [PATCH 02/10] enhance docs for prefix usage

---
 docs/developer_guide.rst | 37 +++++++++++++++++++++++++++++++++----
 1 file changed, 33 insertions(+), 4 deletions(-)

diff --git a/docs/developer_guide.rst b/docs/developer_guide.rst
index dd4988d74..a5c2b8e2c 100644
--- a/docs/developer_guide.rst
+++ b/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-< platform >.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
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

From 53daa681c87f3fb518dc151a9530a637d05df31b Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 25 Jul 2024 15:01:36 +0000
Subject: [PATCH 03/10] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 docs/developer_guide.rst | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/docs/developer_guide.rst b/docs/developer_guide.rst
index a5c2b8e2c..df0d9f25c 100644
--- a/docs/developer_guide.rst
+++ b/docs/developer_guide.rst
@@ -54,15 +54,15 @@ Install the appropriate Python dependencies for your operating system.
 .. 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-< platform >.yml --prefix /mnt/data/nwb-guide
 
 
@@ -78,15 +78,15 @@ Before starting NWB GUIDE, you'll need to ensure that the Python environment is
 .. 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
 
 

From 2f706b96c0e91bd10055ce13c26c15a2ca0f6400 Mon Sep 17 00:00:00 2001
From: codycbakerphd <cbaker9@nd.edu>
Date: Thu, 25 Jul 2024 11:21:18 -0400
Subject: [PATCH 04/10] fix rednering

---
 docs/developer_guide.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/developer_guide.rst b/docs/developer_guide.rst
index a5c2b8e2c..2342899f1 100644
--- a/docs/developer_guide.rst
+++ b/docs/developer_guide.rst
@@ -53,7 +53,7 @@ Install the appropriate Python dependencies for your operating system.
 
 .. 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:
+    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
     
@@ -77,7 +77,7 @@ Before starting NWB GUIDE, you'll need to ensure that the Python environment is
 
 .. note::
 
-    If you had to use the `--prefix` flag in the previous step, then this becomes
+    If you had to use the ``--prefix`` flag in the previous step, then this becomes
     
     .. code-block:: bash
     

From 609dceda67c5ad886f6fede521bfe283e22aec23 Mon Sep 17 00:00:00 2001
From: codycbakerphd <cbaker9@nd.edu>
Date: Thu, 25 Jul 2024 11:24:16 -0400
Subject: [PATCH 05/10] make explicit

---
 docs/developer_guide.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/developer_guide.rst b/docs/developer_guide.rst
index d7d3a7589..ab1c8161a 100644
--- a/docs/developer_guide.rst
+++ b/docs/developer_guide.rst
@@ -63,7 +63,7 @@ Install the appropriate Python dependencies for your operating system.
 
     .. code-block:: bash
 
-        conda env create --file ./environments/environment-< platform >.yml --prefix /mnt/data/nwb-guide
+        conda env create --file ./environments/environment-Linux.yml --prefix /mnt/data/nwb-guide
 
 
 Activate the Python Environment

From 69b7bfec02af49865fa937cd8fa4b29d91416184 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Sun, 28 Jul 2024 14:22:11 -0400
Subject: [PATCH 06/10] try postinstall fix

---
 .github/workflows/testing_dev.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing_dev.yml b/.github/workflows/testing_dev.yml
index 385f13f4d..fc2216211 100644
--- a/.github/workflows/testing_dev.yml
+++ b/.github/workflows/testing_dev.yml
@@ -67,7 +67,7 @@ jobs:
           node-version: 20
 
       - name: Install GUIDE
-        run: npm ci --verbose
+        run: npm ci --verbose --unsafe-perm=true
 
       - if: matrix.os != 'ubuntu-latest'
         name: Run tests

From 550e31d8a5e4de903fac27c8d7ba5a79bd89a67e Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Sun, 28 Jul 2024 17:26:45 -0400
Subject: [PATCH 07/10] try ignore scripts

---
 .github/workflows/testing_dev.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing_dev.yml b/.github/workflows/testing_dev.yml
index fc2216211..bba0cf642 100644
--- a/.github/workflows/testing_dev.yml
+++ b/.github/workflows/testing_dev.yml
@@ -67,7 +67,7 @@ jobs:
           node-version: 20
 
       - name: Install GUIDE
-        run: npm ci --verbose --unsafe-perm=true
+        run: npm ci --verbose --ignore-scripts
 
       - if: matrix.os != 'ubuntu-latest'
         name: Run tests

From afa37525575ef42360e0ecc3dd4ea9bd4a7ba3b2 Mon Sep 17 00:00:00 2001
From: CodyCBakerPhD <codycbakerphd@gmail.com>
Date: Mon, 29 Jul 2024 01:26:16 -0400
Subject: [PATCH 08/10] disable mac on all tests

---
 .github/workflows/testing_dev.yml             | 15 ++++++---
 .../testing_dev_with_live_services.yml        | 15 ++++++---
 .../testing_flask_build_and_dist.yml          | 31 ++++++++++---------
 .github/workflows/testing_pipelines.yml       | 15 ++++++---
 package-lock.json                             |  4 +--
 5 files changed, 48 insertions(+), 32 deletions(-)

diff --git a/.github/workflows/testing_dev.yml b/.github/workflows/testing_dev.yml
index bba0cf642..34e7d1b5b 100644
--- a/.github/workflows/testing_dev.yml
+++ b/.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
diff --git a/.github/workflows/testing_dev_with_live_services.yml b/.github/workflows/testing_dev_with_live_services.yml
index 7dd96ce9c..b44c90c8d 100644
--- a/.github/workflows/testing_dev_with_live_services.yml
+++ b/.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
diff --git a/.github/workflows/testing_flask_build_and_dist.yml b/.github/workflows/testing_flask_build_and_dist.yml
index 6c477d5e4..83f483cf5 100644
--- a/.github/workflows/testing_flask_build_and_dist.yml
+++ b/.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
diff --git a/.github/workflows/testing_pipelines.yml b/.github/workflows/testing_pipelines.yml
index 4467f1872..f8e5022e9 100644
--- a/.github/workflows/testing_pipelines.yml
+++ b/.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
diff --git a/package-lock.json b/package-lock.json
index e5bbb774e..8bd232501 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,12 +1,12 @@
 {
   "name": "nwb-guide",
-  "version": "1.0.0",
+  "version": "1.0.2",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "nwb-guide",
-      "version": "1.0.0",
+      "version": "1.0.2",
       "hasInstallScript": true,
       "license": "MIT",
       "dependencies": {

From 44ded0cdfbb2a2649e27dfdb5f24fb058a45bcf2 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Mon, 29 Jul 2024 01:34:45 -0400
Subject: [PATCH 09/10] revert ignoring postinstall

---
 .github/workflows/testing_dev.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing_dev.yml b/.github/workflows/testing_dev.yml
index bba0cf642..385f13f4d 100644
--- a/.github/workflows/testing_dev.yml
+++ b/.github/workflows/testing_dev.yml
@@ -67,7 +67,7 @@ jobs:
           node-version: 20
 
       - name: Install GUIDE
-        run: npm ci --verbose --ignore-scripts
+        run: npm ci --verbose
 
       - if: matrix.os != 'ubuntu-latest'
         name: Run tests

From 9e844a1cea7c14c54a1c781163a8c0f9837ffd5e Mon Sep 17 00:00:00 2001
From: CodyCBakerPhD <codycbakerphd@gmail.com>
Date: Mon, 29 Jul 2024 03:22:15 -0400
Subject: [PATCH 10/10] might as well remove example data caches too

---
 .github/workflows/example_data_cache.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/example_data_cache.yml b/.github/workflows/example_data_cache.yml
index 5a2b6d9b8..700829876 100644
--- a/.github/workflows/example_data_cache.yml
+++ b/.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: