From ca342ee9d3b8955e6f945c56929122ccbac6966d Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Thu, 14 Sep 2023 05:14:10 -0400
Subject: [PATCH 01/22] Update mac deploy docs and build for x64 and arm64

---
 .github/workflows/Build-and-deploy-mac.yml | 14 +++++++++++++-
 package.json                               | 16 ++++++++++++++--
 2 files changed, 27 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/Build-and-deploy-mac.yml b/.github/workflows/Build-and-deploy-mac.yml
index dd7a77988..7bd6e14c1 100644
--- a/.github/workflows/Build-and-deploy-mac.yml
+++ b/.github/workflows/Build-and-deploy-mac.yml
@@ -50,6 +50,18 @@ jobs:
           # Use Keychain Access to export the certificate as a .p12
           # base64 -i cent.p12 -o base64.txt
           # Open base64.txt and copy the contents to the nwb-guide repository secret for MACOS_CERTIFICATE
+          # For local development, download the appropriate Apple Intermediate Certificate
+          # from https://www.apple.com/certificateauthority/ to make certificate trusted/valid
+          # See https://developer.apple.com/forums/thread/705473
+          # For this, it is Worldwide Developer Relations - G3
+          # Confirm that the certificate now shows up as trusted in Keychain Access
+          # Then go to https://appleid.apple.com/account/manage
+          # and create an App-Specific Password
+          # Use that for local building and in the secrets.APPLE_PASSWORD repository secret
+          # Also review and agree to any pending agreements in
+          # https://appstoreconnect.apple.com/agreements/#/ for Free Apps
+          # and the Apple Developer Program License Agreement, which updates periodically
+
           # Currently this is set up to use Ryan's account and certificate
           p12-file-base64: ${{ secrets.MACOS_CERTIFICATE }}
           p12-password: ${{ secrets.MACOS_CERTIFICATE_PWD }}
@@ -57,6 +69,6 @@ jobs:
       - name: Build and deploy on MAC
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          appleId: ${{ secrets.APPLE_ID }}  # currently this is set to Ryan's Apple ID and password
+          appleId: ${{ secrets.APPLE_ID }}  # currently this is set to Ryan's Apple ID and app-specific password
           appleIdPassword: ${{ secrets.APPLE_PASSWORD }}
         run: npm run deploy:mac
diff --git a/package.json b/package.json
index 3bcb3133a..dd1038059 100644
--- a/package.json
+++ b/package.json
@@ -76,8 +76,20 @@
     "mac": {
       "asar": true,
       "target": [
-        "dmg",
-        "zip"
+        {
+          "target": "dmg",
+          "arch": [
+            "x64",
+            "arm64"
+          ]
+        },
+        {
+          "target": "zip",
+          "arch": [
+            "x64",
+            "arm64"
+          ]
+        }
       ],
       "icon": "src/renderer/assets/img/logo-guide-draft.png",
       "darkModeSupport": false,

From f5aa819432b37f169fa3650fdfb7aa0dad20fa09 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Mon, 18 Sep 2023 11:05:55 -0700
Subject: [PATCH 02/22] Update main.ts

---
 src/main/main.ts | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/main/main.ts b/src/main/main.ts
index 582090189..af34032f6 100755
--- a/src/main/main.ts
+++ b/src/main/main.ts
@@ -126,6 +126,7 @@ const pythonIsClosed = (err = globals.python.latestError) => {
  */
 const getPackagedPath = () => {
   const scriptPath = isWindows ? path.join(__dirname, PY_FLASK_DIST_FOLDER, PYFLASK_BUILD_SUBFOLDER_NAME, `${PYINSTALLER_NAME}.exe`) : path.join(process.resourcesPath, PYFLASK_BUILD_SUBFOLDER_NAME, PYINSTALLER_NAME)
+  console.warn('Packaged Script Path', scriptPath)
   if (fs.existsSync(scriptPath)) return scriptPath;
 };
 
@@ -134,6 +135,8 @@ const createPyProc = async () => {
   return new Promise(async (resolve, reject) => {
 
     let script = getPackagedPath() || path.join(__dirname, PY_FLASK_FOLDER, "app.py");
+    console.warn('Resolved Script Path', script)
+
     await killAllPreviousProcesses();
 
     const defaultPort = PORT as number

From fdaaf79b9c56f873cbdbd8065dbe6f84a0ee5829 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Mon, 18 Sep 2023 14:15:21 -0400
Subject: [PATCH 03/22] Move documentation on codesigning

---
 .github/workflows/Build-and-deploy-mac.yml | 29 ++------------
 docs/developer_guide.rst                   | 46 ++++++++++++++++++++++
 2 files changed, 49 insertions(+), 26 deletions(-)

diff --git a/.github/workflows/Build-and-deploy-mac.yml b/.github/workflows/Build-and-deploy-mac.yml
index b3c6282dd..310b5cc2d 100644
--- a/.github/workflows/Build-and-deploy-mac.yml
+++ b/.github/workflows/Build-and-deploy-mac.yml
@@ -37,37 +37,14 @@ jobs:
 
       - uses: apple-actions/import-codesign-certs@v1
         with:
-          # https://developer.apple.com/account/resources/certificates/add
-          # Sign up for an Apple Developer account (annual fee)
-          # Create a new certificate for Mac development at website above (max 1 certificate)
-          # Create a Certificate Signing Request (CSR) on your Mac --
-          # see https://developer.apple.com/help/account/create-certificates/create-a-certificate-signing-request
-          # Keychain Access > Certificate Assistant > Request a Certificate from a Certificate Authority...
-          # Enter email address, common name
-          # Download the new certificate (.cer file)
-          # Double click the .cer file to install in Keychain Access
-          # Use Keychain Access to export the certificate as a .p12
-          # base64 -i cent.p12 -o base64.txt
-          # Open base64.txt and copy the contents to the nwb-guide repository secret for MACOS_CERTIFICATE
-          # For local development, download the appropriate Apple Intermediate Certificate
-          # from https://www.apple.com/certificateauthority/ to make certificate trusted/valid
-          # See https://developer.apple.com/forums/thread/705473
-          # For this, it is Worldwide Developer Relations - G3
-          # Confirm that the certificate now shows up as trusted in Keychain Access
-          # Then go to https://appleid.apple.com/account/manage
-          # and create an App-Specific Password
-          # Use that for local building and in the secrets.APPLE_PASSWORD repository secret
-          # Also review and agree to any pending agreements in
-          # https://appstoreconnect.apple.com/agreements/#/ for Free Apps
-          # and the Apple Developer Program License Agreement, which updates periodically
-
-          # Currently this is set up to use Ryan's account and certificate
+          # Currently this is set to Ryan's Developer ID certificate
           p12-file-base64: ${{ secrets.MACOS_CERTIFICATE }}
           p12-password: ${{ secrets.MACOS_CERTIFICATE_PWD }}
 
       - name: Build and deploy on MAC
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          appleId: ${{ secrets.APPLE_ID }}  # currently this is set to Ryan's Apple ID and app-specific password
+          # Currently this is set to Ryan's Apple ID and app-specific password
+          appleId: ${{ secrets.APPLE_ID }}
           appleIdPassword: ${{ secrets.APPLE_PASSWORD }}
         run: npm run deploy:mac
diff --git a/docs/developer_guide.rst b/docs/developer_guide.rst
index eb206f426..0602e31a1 100644
--- a/docs/developer_guide.rst
+++ b/docs/developer_guide.rst
@@ -125,3 +125,49 @@ Pre-Commit
 We use an automated pre-commit bot to enforce these on the main repo, but contributions from external forks would either have to grant bot permissions on their own fork (via :pre-commit-bot:`the pre-commit bot website <>`) or run pre-commit manually.
 
 For instructions to install pre-commit, as well as some other minor coding styles we follow, refer to the :neuroconv-coding-style:`NeuroConv style guide <>`.
+
+Code signing on Mac OS
+---------------------------
+
+1. Sign up for an Apple Developer account (99 USD annual fee).
+
+2. Follow steps in https://developer.apple.com/help/account/create-certificates/create-developer-id-certificates/
+    a. Browse current Certificates at https://developer.apple.com/account/resources/certificates/list.
+    b. Click Certificates in the sidebar. On the top left, click the add button (+).
+    c. Under Software, select Developer ID Application.
+    d. Select Profile Type: G2 Sub-CA (Xcode 11.4.1 or later).
+    e. Create a certificate signing request (CSR) by following the steps in https://developer.apple.com/help/account/create-certificates/create-a-certificate-signing-request
+        i. Open Keychain Access.
+        ii. Choose Keychain Access > Certificate Assistant > Request a Certificate from a Certificate Authority.
+        iii. In the Certificate Assistant dialog, enter an email address in the User Email Address field.
+        iv. In the Common Name field, enter a name for the key (for example, John Doe Dev Key). Ryan entered "Ryan Ly".
+        v. Leave the CA Email Address field empty.
+        vi. Choose “Saved to disk”, and click Continue.
+        vii. Save the certificate request file to disk.
+    f. Select the certificate request file (a file with a .certSigningRequest file extension), then click Choose.
+    g. Click Continue, click Download - The certificate file (.cer file) appears in your Downloads folder.
+    h. To install the certificate in your keychain, double-click the downloaded certificate file.
+    i. The certificate appears in the My Certificates category in Keychain Access, but may not be trusted.
+    j. For local development, download the appropriate Apple Intermediate Certificate.
+    k. from https://www.apple.com/certificateauthority/ to make certificate trusted/valid.
+    l. For this, it is Developer ID - G2 (Expiring 09/17/2031 00:00:00 UTC).
+    m. Double-click the downloaded file.
+    n. Confirm that the certificate now shows up as trusted in Keychain Access.
+
+3. Provide a p12 file for notarizing via GitHub Action.
+    a. Open Keychain Access.
+    b. Select the Developer ID Application certificate.
+    c. Choose Keychain Access > Export Items...
+    d. Export the certificate to a file with a password.
+    e. Get a base64 version of the certificate by running: base64 -i Certificate.p12 -o base64.txt
+    f. Open base64.txt and copy the contents to the nwb-guide repository secret MACOS_CERTIFICATE.
+    g. Set the password for the certificate in the nwb-guide repository secret MACOS_CERTIFICATE_PASSWORD.
+
+4. Create an app-specific password for building locally and via the GitHub Action.
+    a. Go to https://appleid.apple.com/account/manage.
+    b. Follow the steps to create an App-Specific Password.
+    c. Use that for local building and in the secrets.APPLE_PASSWORD repository secret.
+
+5. Review and agree to any pending agreements.
+    a. Go to https://appstoreconnect.apple.com/agreements/#/ and agree to pending agreements for Free Apps.
+    b. Review and agree to the Apple Developer Program License Agreement, which updates periodically.
\ No newline at end of file

From d34dd90ada331b9af12a169a13478640c479ff86 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Mon, 18 Sep 2023 14:15:41 -0400
Subject: [PATCH 04/22] Update version to 0.0.6

---
 package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package.json b/package.json
index 3653a3054..9d3d15ed8 100644
--- a/package.json
+++ b/package.json
@@ -1,7 +1,7 @@
 {
   "name": "nwb-guide",
   "productName": "NWB GUIDE",
-  "version": "0.0.5",
+  "version": "0.0.6",
   "description": "",
   "main": "./build/main/main.js",
   "scripts": {

From 8a97fa1be0e828ff1820b5fa6d7110db95da6748 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 18 Sep 2023 18:16:43 +0000
Subject: [PATCH 05/22] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 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 0602e31a1..e191ff894 100644
--- a/docs/developer_guide.rst
+++ b/docs/developer_guide.rst
@@ -170,4 +170,4 @@ Code signing on Mac OS
 
 5. Review and agree to any pending agreements.
     a. Go to https://appstoreconnect.apple.com/agreements/#/ and agree to pending agreements for Free Apps.
-    b. Review and agree to the Apple Developer Program License Agreement, which updates periodically.
\ No newline at end of file
+    b. Review and agree to the Apple Developer Program License Agreement, which updates periodically.

From 61be1292d7b72f06f7ac2fc25f1c3e4994ae0750 Mon Sep 17 00:00:00 2001
From: Ryan Ly <rly@lbl.gov>
Date: Mon, 18 Sep 2023 11:20:24 -0700
Subject: [PATCH 06/22] Revert version bump

---
 package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package.json b/package.json
index 9d3d15ed8..3653a3054 100644
--- a/package.json
+++ b/package.json
@@ -1,7 +1,7 @@
 {
   "name": "nwb-guide",
   "productName": "NWB GUIDE",
-  "version": "0.0.6",
+  "version": "0.0.5",
   "description": "",
   "main": "./build/main/main.js",
   "scripts": {

From 379f0981554ac67955ea97d6f68c787247334ceb Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Mon, 18 Sep 2023 12:04:40 -0700
Subject: [PATCH 07/22] Remove extra subfolder

---
 src/main/main.ts | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/src/main/main.ts b/src/main/main.ts
index af34032f6..508b7016b 100755
--- a/src/main/main.ts
+++ b/src/main/main.ts
@@ -125,8 +125,7 @@ const pythonIsClosed = (err = globals.python.latestError) => {
  * @returns {boolean} True if the app is packaged, false if it is running from a dev version.
  */
 const getPackagedPath = () => {
-  const scriptPath = isWindows ? path.join(__dirname, PY_FLASK_DIST_FOLDER, PYFLASK_BUILD_SUBFOLDER_NAME, `${PYINSTALLER_NAME}.exe`) : path.join(process.resourcesPath, PYFLASK_BUILD_SUBFOLDER_NAME, PYINSTALLER_NAME)
-  console.warn('Packaged Script Path', scriptPath)
+  const scriptPath = isWindows ? path.join(__dirname, PY_FLASK_DIST_FOLDER, `${PYINSTALLER_NAME}.exe`) : path.join(process.resourcesPath, PYFLASK_BUILD_SUBFOLDER_NAME, PYINSTALLER_NAME)
   if (fs.existsSync(scriptPath)) return scriptPath;
 };
 
@@ -135,8 +134,6 @@ const createPyProc = async () => {
   return new Promise(async (resolve, reject) => {
 
     let script = getPackagedPath() || path.join(__dirname, PY_FLASK_FOLDER, "app.py");
-    console.warn('Resolved Script Path', script)
-
     await killAllPreviousProcesses();
 
     const defaultPort = PORT as number

From dd7abc81476672e248c75b1609c12d6106cdcb4e Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 18 Sep 2023 19:21:57 +0000
Subject: [PATCH 08/22] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/stories/pages/Page.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/renderer/src/stories/pages/Page.js b/src/renderer/src/stories/pages/Page.js
index cfd4cc474..49b22071b 100644
--- a/src/renderer/src/stories/pages/Page.js
+++ b/src/renderer/src/stories/pages/Page.js
@@ -64,7 +64,7 @@ export class Page extends LitElement {
         this.beforeTransition();
 
         // Otherwise note unsaved updates if present
-        if (this.unsavedUpdates || ('states' in this.info && !this.info.states.saved)) {
+        if (this.unsavedUpdates || ("states" in this.info && !this.info.states.saved)) {
             if (transition === 1) await this.save(); // Save before a single forward transition
             else {
                 Swal.fire({

From 7065653d41c242aefee8d9113aa955b016525207 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 19 Sep 2023 12:24:53 -0400
Subject: [PATCH 09/22] Update prepare_pyinstaller_spec.py

---
 prepare_pyinstaller_spec.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/prepare_pyinstaller_spec.py b/prepare_pyinstaller_spec.py
index db06d8e91..a71d0923e 100644
--- a/prepare_pyinstaller_spec.py
+++ b/prepare_pyinstaller_spec.py
@@ -20,9 +20,11 @@
 lines[data_line_index] = "datas = [('./paths.config.json', '.'), ('./package.json', '.')]\n"
 
 # Another platform specific difference is the app.py location
-app_py_line_index = next(index for index, line in enumerate(lines) if "app.py" in line)
-app_py_line = "    [f\"{Path('pyflask') / 'app.py'}\"],\n"
-lines[app_py_line_index] = app_py_line
+app_py_line_index, app_py_line = next((index, line) for index, line in enumerate(lines) if "app.py" in line)
+pyflask_start = app_py_line.find("pyflask")  # Can change on certain systems
+injected_app_py_line_base = app_py_line[: (pyflask_start - 1)]
+injected_app_py_line = injected_app_py_line_base + "f\"{Path('pyflask') / 'app.py'}\"],\n"
+lines[app_py_line_index] = injected_app_py_line
 
 with open(file=Path(__file__).parent / "nwb-guide.spec", mode="w") as io:
     io.writelines(lines)

From a4d20cf92e478e49e9564e1cba4bcbab24d60f6d Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Tue, 19 Sep 2023 11:02:51 -0700
Subject: [PATCH 10/22] Ensure processes are closed

---
 src/main/main.ts | 68 +++++++++++++++++++++++++++---------------------
 1 file changed, 38 insertions(+), 30 deletions(-)

diff --git a/src/main/main.ts b/src/main/main.ts
index 582090189..4777e87c6 100755
--- a/src/main/main.ts
+++ b/src/main/main.ts
@@ -223,6 +223,8 @@ let hasBeenOpened = false;
 
 function initialize() {
 
+  if (globals.mainWindow) return // Do not re-initialize if the main window is already declared
+
   makeSingleInstance();
 
   function createWindow() {
@@ -254,42 +256,39 @@ function initialize() {
             })
             .then((responseObject) => {
               let { response } = responseObject;
-              if (response === 0) quit_app()
+              if (response === 0) app.quit();
               else globals.mainWindowReady = true
             });
         }
       } else {
-        await exitPyProc();
-        app.exit();
+        app.quit();
       }
     });
   }
 
-  const quit_app = () => {
-    globals.mainWindow.close();
-    if (!globals.mainWindow.closed) globals.mainWindow.destroy()
-  };
-
   function onAppReady () {
 
-    const promise = createPyProc();
-
-    // Listen after first load
-    promise.then(() => {
-      const chokidar = require('chokidar');
-      chokidar.watch(path.join(__dirname, "../../pyflask"), {
-        ignored:  ['**/__pycache__/**']
-      }).on('all', async (event: string) => {
-        if (event === 'change' && !globals.python.restart) {
-          globals.python.restart = true
-          await exitPyProc();
-          setTimeout(async () => {
-            await createPyProc();
-            globals.python.restart = false
-          }, 1000)
-        }
-      });
-    })
+    // Only create one python process
+    if (!pyflaskProcess) {
+      const promise = createPyProc();
+
+      // Listen after first load
+      promise.then(() => {
+        const chokidar = require('chokidar');
+        chokidar.watch(path.join(__dirname, "../../pyflask"), {
+          ignored:  ['**/__pycache__/**']
+        }).on('all', async (event: string) => {
+          if (event === 'change' && !globals.python.restart) {
+            globals.python.restart = true
+            await exitPyProc();
+            setTimeout(async () => {
+              await createPyProc();
+              globals.python.restart = false
+            }, 1000)
+          }
+        });
+      })
+    }
 
     const windowOptions = {
       minWidth: 1121,
@@ -394,13 +393,22 @@ app.on('activate', () => {
   if (BrowserWindow.getAllWindows().length === 0) initialize()
 })
 
-app.on("window-all-closed", async () => {
-  if (process.platform != 'darwin') {
-    await exitPyProc();
-    app.quit();
+app.on('will-quit', async () => {
+  try {
+    await exitPyProc()
+    if (globals.mainWindow) {
+      globals.mainWindow.close();
+      if (!globals.mainWindow.closed) globals.mainWindow.destroy()
+    }
+  } catch (err) {
+    console.error(err);
   }
 });
 
+app.on("window-all-closed", async () => {
+  if (process.platform != 'darwin') app.quit();
+});
+
 // app.on("will-quit", () => app.quit());
 
 app.on("open-file", onFileOpened)

From 3631687a0295e7e8761c28f5c04c7a657441ce92 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Tue, 19 Sep 2023 11:04:13 -0700
Subject: [PATCH 11/22] Update main.ts

---
 src/main/main.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/main.ts b/src/main/main.ts
index 4777e87c6..f286dfe1c 100755
--- a/src/main/main.ts
+++ b/src/main/main.ts
@@ -190,7 +190,7 @@ const exitPyProc = async () => {
     "/t",
   ])  // Windows does not properly shut off the python server process. This ensures it is killed.
 
-  else pyflaskProcess.kill()
+  pyflaskProcess.kill() // Try killing twice on Windows
 
   pyflaskProcess = null;
 };

From bbdfe1106b42136e3dc4b319d5ca0848ff39f7d7 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Tue, 19 Sep 2023 11:05:41 -0700
Subject: [PATCH 12/22] Re-add logs

---
 src/main/main.ts | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/main/main.ts b/src/main/main.ts
index 508b7016b..a108cbf66 100755
--- a/src/main/main.ts
+++ b/src/main/main.ts
@@ -126,6 +126,7 @@ const pythonIsClosed = (err = globals.python.latestError) => {
  */
 const getPackagedPath = () => {
   const scriptPath = isWindows ? path.join(__dirname, PY_FLASK_DIST_FOLDER, `${PYINSTALLER_NAME}.exe`) : path.join(process.resourcesPath, PYFLASK_BUILD_SUBFOLDER_NAME, PYINSTALLER_NAME)
+  console.warn('Packaged Script Path', scriptPath)
   if (fs.existsSync(scriptPath)) return scriptPath;
 };
 
@@ -134,6 +135,8 @@ const createPyProc = async () => {
   return new Promise(async (resolve, reject) => {
 
     let script = getPackagedPath() || path.join(__dirname, PY_FLASK_FOLDER, "app.py");
+    console.warn('Resolved Script Path', script)
+
     await killAllPreviousProcesses();
 
     const defaultPort = PORT as number

From 88009720bf15fb9175bf2b991c8f1d6ae7be8c8c Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 20 Sep 2023 12:50:12 -0400
Subject: [PATCH 13/22] Update testing.yml

---
 .github/workflows/testing.yml | 11 ++---------
 1 file changed, 2 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 0cfb20d1b..052813f42 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -27,17 +27,14 @@ jobs:
           - python-version: "3.9"
             os: ubuntu-latest
             label: environments/environment-Linux.yml
-            prefix: /usr/share/miniconda3/envs/env-electron-python
 
           - python-version: "3.10"
             os: macos-latest
             label: environments/environment-Mac.yml
-            prefix: /Users/runner/miniconda3/envs/env-electron-python
 
           - python-version: "3.9"
             os: windows-latest
             label: environments/environment-Windows.yml
-            prefix: C:\Miniconda3\envs\env-electron-python
 
 
     steps:
@@ -50,7 +47,7 @@ jobs:
         with:
           miniforge-variant: Mambaforge
           miniforge-version: latest
-          activate-environment: env-electron-python
+          activate-environment: nwb-guide
           use-mamba: true
 
       - name: Set cache date
@@ -62,11 +59,7 @@ jobs:
         uses: actions/cache@v2
         with:
           path: ${{ env.CONDA }}/envs
-          key:
-            conda-${{ runner.os }}-${{ runner.arch }}-${{steps.get-date.outputs.today }}-${{ hashFiles(matrix.label) }}-${{ env.CACHE_NUMBER }}
-        env:
-          # Increase this value to reset cache if environment file has not changed
-          CACHE_NUMBER: 0
+          key: conda-${{ runner.os }}-${{ runner.arch }}-${{steps.get-date.outputs.today }}-${{ hashFiles(matrix.label) }}-${{ env.CACHE_NUMBER }}
         id: cache
 
       - name: Update environment

From 1e0ca3225f8dbac99a2b62263ed7ce190c52c494 Mon Sep 17 00:00:00 2001
From: Garrett Michael Flynn <46533749+GarrettMFlynn@users.noreply.github.com>
Date: Wed, 20 Sep 2023 10:21:11 -0700
Subject: [PATCH 14/22] Update main.ts

---
 src/main/main.ts | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/src/main/main.ts b/src/main/main.ts
index a108cbf66..53c027eb2 100755
--- a/src/main/main.ts
+++ b/src/main/main.ts
@@ -125,8 +125,7 @@ const pythonIsClosed = (err = globals.python.latestError) => {
  * @returns {boolean} True if the app is packaged, false if it is running from a dev version.
  */
 const getPackagedPath = () => {
-  const scriptPath = isWindows ? path.join(__dirname, PY_FLASK_DIST_FOLDER, `${PYINSTALLER_NAME}.exe`) : path.join(process.resourcesPath, PYFLASK_BUILD_SUBFOLDER_NAME, PYINSTALLER_NAME)
-  console.warn('Packaged Script Path', scriptPath)
+  const scriptPath = isWindows ? path.join(__dirname, PY_FLASK_DIST_FOLDER, PYINSTALLER_NAME, `${PYINSTALLER_NAME}.exe`) : path.join(process.resourcesPath, PYFLASK_BUILD_SUBFOLDER_NAME, PYINSTALLER_NAME)
   if (fs.existsSync(scriptPath)) return scriptPath;
 };
 
@@ -135,8 +134,6 @@ const createPyProc = async () => {
   return new Promise(async (resolve, reject) => {
 
     let script = getPackagedPath() || path.join(__dirname, PY_FLASK_FOLDER, "app.py");
-    console.warn('Resolved Script Path', script)
-
     await killAllPreviousProcesses();
 
     const defaultPort = PORT as number

From 02dba465a1cdd559028da0f56b0420ba9722ca2e Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 20 Sep 2023 13:52:44 -0400
Subject: [PATCH 15/22] test bump

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

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 052813f42..5b414c18c 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -9,7 +9,7 @@ concurrency:  # Cancel previous workflows on the same pull request
   cancel-in-progress: true
 
 env:
-  CACHE_NUMBER: 1  # increase to reset cache manually
+  CACHE_NUMBER: 2  # increase to reset cache manually
 
 jobs:
   testing:

From 761e3fbe43e219c9aec79355515c6649155f1194 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 20 Sep 2023 14:03:39 -0400
Subject: [PATCH 16/22] Update testing.yml

---
 .github/workflows/testing.yml | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 5b414c18c..a56f4e4e8 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -62,10 +62,15 @@ jobs:
           key: conda-${{ runner.os }}-${{ runner.arch }}-${{steps.get-date.outputs.today }}-${{ hashFiles(matrix.label) }}-${{ env.CACHE_NUMBER }}
         id: cache
 
-      - name: Update environment
-        run:
-          mamba env update -n env-electron-python -f ${{ matrix.label }}
-        if: steps.cache.outputs.cache-hit != 'true'
+      - if: steps.cache.outputs.cache-hit != 'true'
+        name: Create and activate environment
+        run: |
+          mamba env create -n nwb-guide -f ${{ matrix.label }}
+          mamba activate nwb-guide
+
+      - if: steps.cache.outputs.cache-hit == 'true'
+        name: Activate environment
+        run: mamba activate nwb-guide
 
       - name: Use Node.js 18
         uses: actions/setup-node@v3

From af34c42b8442837734558a6c950ed511294fba34 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 20 Sep 2023 14:07:09 -0400
Subject: [PATCH 17/22] Update testing.yml

---
 .github/workflows/testing.yml | 17 ++++-------------
 1 file changed, 4 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index a56f4e4e8..0ef322e2c 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -24,16 +24,13 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
         include:
-          - python-version: "3.9"
-            os: ubuntu-latest
+          - os: ubuntu-latest
             label: environments/environment-Linux.yml
 
-          - python-version: "3.10"
-            os: macos-latest
+          - os: macos-latest
             label: environments/environment-Mac.yml
 
-          - python-version: "3.9"
-            os: windows-latest
+          - os: windows-latest
             label: environments/environment-Windows.yml
 
 
@@ -64,13 +61,7 @@ jobs:
 
       - if: steps.cache.outputs.cache-hit != 'true'
         name: Create and activate environment
-        run: |
-          mamba env create -n nwb-guide -f ${{ matrix.label }}
-          mamba activate nwb-guide
-
-      - if: steps.cache.outputs.cache-hit == 'true'
-        name: Activate environment
-        run: mamba activate nwb-guide
+        run: mamba env update -n nwb-guide -f ${{ matrix.label }}
 
       - name: Use Node.js 18
         uses: actions/setup-node@v3

From c4564840b8cf37842f821f78cf4dbffd972c74ab Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Wed, 20 Sep 2023 15:44:28 -0700
Subject: [PATCH 18/22] Fix error in updating project name, edit error msg

---
 src/renderer/src/progress/update.js                  | 12 +++++-------
 .../pages/guided-mode/setup/GuidedNewDatasetInfo.js  |  2 +-
 2 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/src/renderer/src/progress/update.js b/src/renderer/src/progress/update.js
index 8756db83a..4983aef65 100644
--- a/src/renderer/src/progress/update.js
+++ b/src/renderer/src/progress/update.js
@@ -2,15 +2,15 @@ import { updateURLParams } from "../../utils/url.js";
 import { guidedProgressFilePath } from "../dependencies/simple.js";
 import { fs } from "../electron/index.js";
 import { joinPath } from "../globals.js";
-import { get } from "./index.js";
+import { get, hasEntry } from "./index.js";
 
 export const update = (newDatasetName, previousDatasetName) => {
-    //If updataing the dataset, update the old banner image path with a new one
+    //If updating the dataset, update the old banner image path with a new one
     if (previousDatasetName) {
-        if (previousDatasetName === newDatasetName) return "No changes made to dataset name";
+        if (previousDatasetName === newDatasetName) return;
 
         if (hasEntry(newDatasetName))
-            throw new Error("An existing progress file already exists with that name. Please choose a different name.");
+            throw new Error("An existing project already exists with that name. Please choose a different name.");
 
         // update old progress file with new dataset name
         const oldProgressFilePath = `${guidedProgressFilePath}/${previousDatasetName}.json`;
@@ -20,9 +20,7 @@ export const update = (newDatasetName, previousDatasetName) => {
             localStorage.setItem(newProgressFilePath, localStorage.getItem(oldProgressFilePath));
             localStorage.removeItem(oldProgressFilePath);
         }
-
-        return "Dataset name updated";
-    } else throw new Error("No previous dataset name provided");
+    } else throw new Error("No previous project name provided");
 };
 export const updateAppProgress = (
     pageId,
diff --git a/src/renderer/src/stories/pages/guided-mode/setup/GuidedNewDatasetInfo.js b/src/renderer/src/stories/pages/guided-mode/setup/GuidedNewDatasetInfo.js
index e39b8fe4e..cdb2c6f62 100644
--- a/src/renderer/src/stories/pages/guided-mode/setup/GuidedNewDatasetInfo.js
+++ b/src/renderer/src/stories/pages/guided-mode/setup/GuidedNewDatasetInfo.js
@@ -61,7 +61,7 @@ export class GuidedNewDatasetPage extends Page {
                 const has = await hasEntry(name);
                 if (has) {
                     this.notify(
-                        "An existing progress file already exists with that name. Please choose a different name.",
+                        "An existing project already exists with that name. Please choose a different name.",
                         "error"
                     );
                     return;

From f643c12d0ebb4c5e2b8fb7bf1fd97f0467a0ea75 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Thu, 21 Sep 2023 10:37:54 -0700
Subject: [PATCH 19/22] Change update to rename

---
 src/renderer/src/progress/update.js                          | 5 +++--
 .../stories/pages/guided-mode/setup/GuidedNewDatasetInfo.js  | 4 ++--
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/renderer/src/progress/update.js b/src/renderer/src/progress/update.js
index 8756db83a..8c5fc7e30 100644
--- a/src/renderer/src/progress/update.js
+++ b/src/renderer/src/progress/update.js
@@ -4,8 +4,8 @@ import { fs } from "../electron/index.js";
 import { joinPath } from "../globals.js";
 import { get } from "./index.js";
 
-export const update = (newDatasetName, previousDatasetName) => {
-    //If updataing the dataset, update the old banner image path with a new one
+export const rename = (newDatasetName, previousDatasetName) => {
+    //If updating the dataset, update the old banner image path with a new one
     if (previousDatasetName) {
         if (previousDatasetName === newDatasetName) return "No changes made to dataset name";
 
@@ -24,6 +24,7 @@ export const update = (newDatasetName, previousDatasetName) => {
         return "Dataset name updated";
     } else throw new Error("No previous dataset name provided");
 };
+
 export const updateAppProgress = (
     pageId,
     dataOrProjectName = {},
diff --git a/src/renderer/src/stories/pages/guided-mode/setup/GuidedNewDatasetInfo.js b/src/renderer/src/stories/pages/guided-mode/setup/GuidedNewDatasetInfo.js
index e39b8fe4e..7b081e41c 100644
--- a/src/renderer/src/stories/pages/guided-mode/setup/GuidedNewDatasetInfo.js
+++ b/src/renderer/src/stories/pages/guided-mode/setup/GuidedNewDatasetInfo.js
@@ -1,5 +1,5 @@
 import { html } from "lit";
-import { global, hasEntry, update } from "../../../../progress/index.js";
+import { global, hasEntry, rename } from "../../../../progress/index.js";
 import { JSONSchemaForm } from "../../../JSONSchemaForm.js";
 import { Page } from "../../Page.js";
 import { validateOnChange } from "../../../../validation/index.js";
@@ -50,7 +50,7 @@ export class GuidedNewDatasetPage extends Page {
             // Update existing progress file
             if (globalState.initialized) {
                 try {
-                    const res = update(name, globalState.name);
+                    const res = rename(name, globalState.name);
                     if (typeof res === "string") this.notify(res);
                     if (res === false) return;
                 } catch (e) {

From b9e67f1a8c76c8bb6293603e6ef6ebbd28b25255 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Thu, 21 Sep 2023 10:38:22 -0700
Subject: [PATCH 20/22] Add test

---
 src/renderer/src/progress/index.js      | 23 +++++---------------
 src/renderer/src/progress/operations.js | 23 ++++++++++++++++++++
 tests/progress.test.ts                  | 29 +++++++++++++++++++++++--
 3 files changed, 55 insertions(+), 20 deletions(-)
 create mode 100644 src/renderer/src/progress/operations.js

diff --git a/src/renderer/src/progress/index.js b/src/renderer/src/progress/index.js
index 8e39c7e97..7de0bb38e 100644
--- a/src/renderer/src/progress/index.js
+++ b/src/renderer/src/progress/index.js
@@ -14,6 +14,8 @@ import { merge } from "../stories/pages/utils.js";
 import { updateAppProgress, updateFile } from "./update.js";
 import { updateURLParams } from "../../utils/url.js";
 
+import * as operations from './operations'
+
 export * from "./update";
 
 class GlobalAppConfig {
@@ -56,6 +58,8 @@ export const save = (page, overrides = {}) => {
 export const getEntries = () => {
     if (fs && !fs.existsSync(guidedProgressFilePath)) fs.mkdirSync(guidedProgressFilePath, { recursive: true }); //Check if progress folder exists. If not, create it.
     const progressFiles = fs ? fs.readdirSync(guidedProgressFilePath) : Object.keys(localStorage);
+    console.log(progressFiles)
+
     return progressFiles.filter((path) => path.slice(-5) === ".json");
 };
 
@@ -122,24 +126,7 @@ export const remove = async (name) => {
         focusCancel: true,
     });
 
-    if (result.isConfirmed) {
-        //Get the path of the progress file to delete
-        const progressFilePathToDelete = joinPath(guidedProgressFilePath, name + ".json");
-
-        //delete the progress file
-        if (fs) fs.unlinkSync(progressFilePathToDelete);
-        else localStorage.removeItem(progressFilePathToDelete);
-
-        if (fs) {
-            // delete default stub location
-            fs.rmSync(joinPath(stubSaveFolderPath, name), { recursive: true, force: true });
-
-            // delete default conversion location
-            fs.rmSync(joinPath(conversionSaveFolderPath, name), { recursive: true, force: true });
-        }
-
-        return true;
-    }
+    if (result.isConfirmed) return operations.remove(name)
 
     return false;
 };
diff --git a/src/renderer/src/progress/operations.js b/src/renderer/src/progress/operations.js
new file mode 100644
index 000000000..7cd8df54d
--- /dev/null
+++ b/src/renderer/src/progress/operations.js
@@ -0,0 +1,23 @@
+import { joinPath } from "../globals";
+import { conversionSaveFolderPath, guidedProgressFilePath, stubSaveFolderPath } from "../dependencies/simple";
+import { fs } from "../electron";
+
+
+export const remove = (name) => {
+     //Get the path of the progress file to delete
+     const progressFilePathToDelete = joinPath(guidedProgressFilePath, name + ".json");
+
+     //delete the progress file
+     if (fs) fs.unlinkSync(progressFilePathToDelete);
+     else localStorage.removeItem(progressFilePathToDelete);
+
+     if (fs) {
+         // delete default stub location
+         fs.rmSync(joinPath(stubSaveFolderPath, name), { recursive: true, force: true });
+
+         // delete default conversion location
+         fs.rmSync(joinPath(conversionSaveFolderPath, name), { recursive: true, force: true });
+     }
+
+     return true;
+}
\ No newline at end of file
diff --git a/tests/progress.test.ts b/tests/progress.test.ts
index 52f68b634..4e8e9da72 100644
--- a/tests/progress.test.ts
+++ b/tests/progress.test.ts
@@ -1,4 +1,29 @@
-import { test } from 'vitest'
-import { updateAppProgress } from '../src/renderer/src/progress/update'
+import { expect, test } from 'vitest'
+import { updateAppProgress, updateFile, rename } from '../src/renderer/src/progress/update'
+import { get } from '../src/renderer/src/progress'
+import { remove } from '../src/renderer/src/progress/operations'
 
 test('updates to app progress do not fail', () => updateAppProgress('/', {}))
+
+const initialName = '.progressTestPipelineName'
+const renameName = initialName + 2
+const info = { random: Math.random() }
+
+// Remove before tests
+remove(initialName)
+remove(renameName)
+
+// create pipeline
+test('pipeline creation works', () => {
+    updateFile(initialName, () => info)
+    const result = get(initialName)
+    expect(result.random).toEqual(info.random) // NOTE: Result has an extra lastModified field
+})
+
+// rename pipeline
+test('pipeline renaming works', () => rename(renameName, initialName))
+
+// delete pipeline
+test('pipeline deletion works', () => remove(renameName))
+
+

From 98b2077126f933cd9aa905c3606150939476fa4e Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Thu, 21 Sep 2023 10:38:48 -0700
Subject: [PATCH 21/22] Update index.js

---
 src/renderer/src/progress/index.js | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/renderer/src/progress/index.js b/src/renderer/src/progress/index.js
index 7de0bb38e..f303dabd2 100644
--- a/src/renderer/src/progress/index.js
+++ b/src/renderer/src/progress/index.js
@@ -58,8 +58,6 @@ export const save = (page, overrides = {}) => {
 export const getEntries = () => {
     if (fs && !fs.existsSync(guidedProgressFilePath)) fs.mkdirSync(guidedProgressFilePath, { recursive: true }); //Check if progress folder exists. If not, create it.
     const progressFiles = fs ? fs.readdirSync(guidedProgressFilePath) : Object.keys(localStorage);
-    console.log(progressFiles)
-
     return progressFiles.filter((path) => path.slice(-5) === ".json");
 };
 

From e7af457fa38b356c23bada5e15f42a9a533e6c6d Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 21 Sep 2023 17:39:19 +0000
Subject: [PATCH 22/22] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/renderer/src/progress/index.js      |  4 ++--
 src/renderer/src/progress/operations.js | 27 ++++++++++++-------------
 tests/progress.test.ts                  |  2 --
 3 files changed, 15 insertions(+), 18 deletions(-)

diff --git a/src/renderer/src/progress/index.js b/src/renderer/src/progress/index.js
index f303dabd2..212954f47 100644
--- a/src/renderer/src/progress/index.js
+++ b/src/renderer/src/progress/index.js
@@ -14,7 +14,7 @@ import { merge } from "../stories/pages/utils.js";
 import { updateAppProgress, updateFile } from "./update.js";
 import { updateURLParams } from "../../utils/url.js";
 
-import * as operations from './operations'
+import * as operations from "./operations";
 
 export * from "./update";
 
@@ -124,7 +124,7 @@ export const remove = async (name) => {
         focusCancel: true,
     });
 
-    if (result.isConfirmed) return operations.remove(name)
+    if (result.isConfirmed) return operations.remove(name);
 
     return false;
 };
diff --git a/src/renderer/src/progress/operations.js b/src/renderer/src/progress/operations.js
index 7cd8df54d..20ec92b2c 100644
--- a/src/renderer/src/progress/operations.js
+++ b/src/renderer/src/progress/operations.js
@@ -2,22 +2,21 @@ import { joinPath } from "../globals";
 import { conversionSaveFolderPath, guidedProgressFilePath, stubSaveFolderPath } from "../dependencies/simple";
 import { fs } from "../electron";
 
-
 export const remove = (name) => {
-     //Get the path of the progress file to delete
-     const progressFilePathToDelete = joinPath(guidedProgressFilePath, name + ".json");
+    //Get the path of the progress file to delete
+    const progressFilePathToDelete = joinPath(guidedProgressFilePath, name + ".json");
 
-     //delete the progress file
-     if (fs) fs.unlinkSync(progressFilePathToDelete);
-     else localStorage.removeItem(progressFilePathToDelete);
+    //delete the progress file
+    if (fs) fs.unlinkSync(progressFilePathToDelete);
+    else localStorage.removeItem(progressFilePathToDelete);
 
-     if (fs) {
-         // delete default stub location
-         fs.rmSync(joinPath(stubSaveFolderPath, name), { recursive: true, force: true });
+    if (fs) {
+        // delete default stub location
+        fs.rmSync(joinPath(stubSaveFolderPath, name), { recursive: true, force: true });
 
-         // delete default conversion location
-         fs.rmSync(joinPath(conversionSaveFolderPath, name), { recursive: true, force: true });
-     }
+        // delete default conversion location
+        fs.rmSync(joinPath(conversionSaveFolderPath, name), { recursive: true, force: true });
+    }
 
-     return true;
-}
\ No newline at end of file
+    return true;
+};
diff --git a/tests/progress.test.ts b/tests/progress.test.ts
index 4e8e9da72..f00782f73 100644
--- a/tests/progress.test.ts
+++ b/tests/progress.test.ts
@@ -25,5 +25,3 @@ test('pipeline renaming works', () => rename(renameName, initialName))
 
 // delete pipeline
 test('pipeline deletion works', () => remove(renameName))
-
-