From 0a0b4b0853f342c2f860c53616e654d4cc18db9e Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 16 Aug 2023 23:30:05 -0400
Subject: [PATCH 01/14] Create pyflask-build-and-dist-tests.yml

---
 .../pyflask-build-and-dist-tests.yml          | 95 +++++++++++++++++++
 1 file changed, 95 insertions(+)
 create mode 100644 .github/workflows/pyflask-build-and-dist-tests.yml

diff --git a/.github/workflows/pyflask-build-and-dist-tests.yml b/.github/workflows/pyflask-build-and-dist-tests.yml
new file mode 100644
index 000000000..a6c205dc9
--- /dev/null
+++ b/.github/workflows/pyflask-build-and-dist-tests.yml
@@ -0,0 +1,95 @@
+name: PyFlask build and distributable tests
+on:
+  schedule:
+    - cron: "0 16 * * *"  # Daily at noon EST
+  pull_request:
+
+# Cancel previous workflows on the same pull request
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  CACHE_NUMBER: 1  # increase to reset cache manually
+
+jobs:
+  testing:
+    name: PyFlask build and distributable tests on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        include:
+          - python-version: "3.9"
+            os: ubuntu-latest
+            label: environments/environment-Linux.yml
+            prefix: /usr/share/miniconda3/envs/nwb-guide
+            shorthand: unix
+
+          - python-version: "3.10"
+            os: macos-latest
+            label: environments/environment-Mac.yml
+            prefix: /Users/runner/miniconda3/envs/nwb-guide
+            shorthand: unix
+
+          - python-version: "3.9"
+            os: windows-latest
+            label: environments/environment-Windows.yml
+            prefix: C:\Miniconda3\envs\nwb-guide
+            shorthand: win
+
+    steps:
+      - uses: actions/checkout@v3
+      - run: git fetch --prune --unshallow --tags
+
+      # see https://github.com/conda-incubator/setup-miniconda#caching-environments
+      - name: Setup Mambaforge
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+          activate-environment: nwb-guide
+          use-mamba: true
+
+      - name: Set cache date
+        id: get-date
+        run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
+        shell: bash
+
+      - name: Cache Mamba env
+        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:
+          CACHE_NUMBER: ${{ CACHE_NUMBER }}
+        id: cache
+
+      - if: steps.cache.outputs.cache-hit != 'true'
+        name: Update environment
+        run: mamba env update -n env-electron-python -f ${{ matrix.label }}
+
+      - name: Setup Node
+        uses: actions/setup-node@v3
+        with:
+          node-version: "16"
+
+      - name: Build PyFlask distribution
+        run: npm run build:flask:${{ matrix.shorthand }}
+
+      - if: matrix.os == "windows-latest"
+        name: Run test on build executable
+        run: node tests/testPyinstallerExecutable.js ./build/nwb-guide/nwb-guide.exe
+
+      - if: matrix.os != "windows-latest"
+        name: Run test on build executable
+        run: node tests/testPyinstallerExecutable.js ./build/nwb-guide/nwb-guide
+
+      - name: Run test on distributed executable
+        run: node tests/testPyinstallerExecutable.js

From fb98ceb4824a0f5a6bb4f8e1bedd43529b1faf4a Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 16 Aug 2023 23:31:34 -0400
Subject: [PATCH 02/14] try to trigger for testing

---
 .github/workflows/pyflask-build-and-dist-tests.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/pyflask-build-and-dist-tests.yml b/.github/workflows/pyflask-build-and-dist-tests.yml
index a6c205dc9..6a91131a5 100644
--- a/.github/workflows/pyflask-build-and-dist-tests.yml
+++ b/.github/workflows/pyflask-build-and-dist-tests.yml
@@ -3,6 +3,8 @@ on:
   schedule:
     - cron: "0 16 * * *"  # Daily at noon EST
   pull_request:
+  push:
+  workflow_dispatch:
 
 # Cancel previous workflows on the same pull request
 concurrency:

From fdcd06e70068bbe5981373681b31880e6fcb6207 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 16 Aug 2023 23:33:01 -0400
Subject: [PATCH 03/14] no dice

---
 .github/workflows/pyflask-build-and-dist-tests.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/pyflask-build-and-dist-tests.yml b/.github/workflows/pyflask-build-and-dist-tests.yml
index 6a91131a5..1cfebac15 100644
--- a/.github/workflows/pyflask-build-and-dist-tests.yml
+++ b/.github/workflows/pyflask-build-and-dist-tests.yml
@@ -3,7 +3,6 @@ on:
   schedule:
     - cron: "0 16 * * *"  # Daily at noon EST
   pull_request:
-  push:
   workflow_dispatch:
 
 # Cancel previous workflows on the same pull request

From 310761fa074fc97c37f07a3d71075ea0cf30f1a8 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Thu, 17 Aug 2023 22:51:10 -0400
Subject: [PATCH 04/14] fix typo

---
 .github/workflows/pyflask-build-and-dist-tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pyflask-build-and-dist-tests.yml b/.github/workflows/pyflask-build-and-dist-tests.yml
index 1cfebac15..6c388307d 100644
--- a/.github/workflows/pyflask-build-and-dist-tests.yml
+++ b/.github/workflows/pyflask-build-and-dist-tests.yml
@@ -69,7 +69,7 @@ jobs:
           key:
             conda-${{ runner.os }}-${{ runner.arch }}-${{steps.get-date.outputs.today }}-${{ hashFiles(matrix.label) }}-${{ env.CACHE_NUMBER }}
         env:
-          CACHE_NUMBER: ${{ CACHE_NUMBER }}
+          CACHE_NUMBER: ${{ env.CACHE_NUMBER }}
         id: cache
 
       - if: steps.cache.outputs.cache-hit != 'true'

From 5595bc0518ae86a6a24879b75c8b59a1d5948440 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Thu, 17 Aug 2023 22:53:01 -0400
Subject: [PATCH 05/14] single quotes

---
 .github/workflows/pyflask-build-and-dist-tests.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pyflask-build-and-dist-tests.yml b/.github/workflows/pyflask-build-and-dist-tests.yml
index 6c388307d..d1bee9a50 100644
--- a/.github/workflows/pyflask-build-and-dist-tests.yml
+++ b/.github/workflows/pyflask-build-and-dist-tests.yml
@@ -84,11 +84,11 @@ jobs:
       - name: Build PyFlask distribution
         run: npm run build:flask:${{ matrix.shorthand }}
 
-      - if: matrix.os == "windows-latest"
+      - if: matrix.os == 'windows-latest'
         name: Run test on build executable
         run: node tests/testPyinstallerExecutable.js ./build/nwb-guide/nwb-guide.exe
 
-      - if: matrix.os != "windows-latest"
+      - if: matrix.os != 'windows-latest'
         name: Run test on build executable
         run: node tests/testPyinstallerExecutable.js ./build/nwb-guide/nwb-guide
 

From 0e69c2540ae8510f7587ec48433402a14f1edd61 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Thu, 17 Aug 2023 22:55:03 -0400
Subject: [PATCH 06/14] fix mamba env reference

---
 .github/workflows/pyflask-build-and-dist-tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pyflask-build-and-dist-tests.yml b/.github/workflows/pyflask-build-and-dist-tests.yml
index d1bee9a50..0c867a9b5 100644
--- a/.github/workflows/pyflask-build-and-dist-tests.yml
+++ b/.github/workflows/pyflask-build-and-dist-tests.yml
@@ -74,7 +74,7 @@ jobs:
 
       - if: steps.cache.outputs.cache-hit != 'true'
         name: Update environment
-        run: mamba env update -n env-electron-python -f ${{ matrix.label }}
+        run: mamba env update -n nwb-guide -f ${{ matrix.label }}
 
       - name: Setup Node
         uses: actions/setup-node@v3

From 2d3bd1fbd96cb8cf6eb4ba89eb7fc912cb19107d Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Thu, 17 Aug 2023 22:59:33 -0400
Subject: [PATCH 07/14] restore env path base

---
 .github/workflows/pyflask-build-and-dist-tests.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/pyflask-build-and-dist-tests.yml b/.github/workflows/pyflask-build-and-dist-tests.yml
index 0c867a9b5..4f7ece026 100644
--- a/.github/workflows/pyflask-build-and-dist-tests.yml
+++ b/.github/workflows/pyflask-build-and-dist-tests.yml
@@ -28,19 +28,19 @@ jobs:
         include:
           - python-version: "3.9"
             os: ubuntu-latest
-            label: environments/environment-Linux.yml
+            label: tools/anaconda-env/environment-Linux.yml
             prefix: /usr/share/miniconda3/envs/nwb-guide
             shorthand: unix
 
           - python-version: "3.10"
             os: macos-latest
-            label: environments/environment-Mac.yml
+            label: tools/anaconda-env/environment-Mac.yml
             prefix: /Users/runner/miniconda3/envs/nwb-guide
             shorthand: unix
 
           - python-version: "3.9"
             os: windows-latest
-            label: environments/environment-Windows.yml
+            label: tools/anaconda-env/environment-Windows.yml
             prefix: C:\Miniconda3\envs\nwb-guide
             shorthand: win
 
@@ -74,7 +74,7 @@ jobs:
 
       - if: steps.cache.outputs.cache-hit != 'true'
         name: Update environment
-        run: mamba env update -n nwb-guide -f ${{ matrix.label }}
+        run: mamba env create -f ${{ matrix.label }}
 
       - name: Setup Node
         uses: actions/setup-node@v3

From 2b5afc6a39d223ed4b2e9ad6a0a82c21dcf60cd3 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Thu, 17 Aug 2023 23:09:15 -0400
Subject: [PATCH 08/14] try update on the file

---
 .github/workflows/pyflask-build-and-dist-tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pyflask-build-and-dist-tests.yml b/.github/workflows/pyflask-build-and-dist-tests.yml
index 4f7ece026..30762a676 100644
--- a/.github/workflows/pyflask-build-and-dist-tests.yml
+++ b/.github/workflows/pyflask-build-and-dist-tests.yml
@@ -74,7 +74,7 @@ jobs:
 
       - if: steps.cache.outputs.cache-hit != 'true'
         name: Update environment
-        run: mamba env create -f ${{ matrix.label }}
+        run: mamba env update -f ${{ matrix.label }}
 
       - name: Setup Node
         uses: actions/setup-node@v3

From 9522bc1a53edf00a9884d9c193efc4eec8e75b17 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Thu, 17 Aug 2023 23:22:44 -0400
Subject: [PATCH 09/14] add error throws

---
 tests/testPyinstallerExecutable.js | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/testPyinstallerExecutable.js b/tests/testPyinstallerExecutable.js
index fd571429e..588ed871d 100644
--- a/tests/testPyinstallerExecutable.js
+++ b/tests/testPyinstallerExecutable.js
@@ -32,10 +32,12 @@ function handleProcess(proc, id = "process") {
 
         proc.on("error", (error) => {
             console.error(`[${id}] error: ${error.message}`);
+            throw new Error("The distributable pyflask failed to run!");
         });
 
         proc.on("close", (code) => {
             console.error(`[${id}] exit: ${code}`);
+            throw new Error("The distributable pyflask failed to run!");
         });
     } else console.error("child process failed to start on port" + port);
 }

From 3377271dbfc5368831b585eb5de8ac0e2916f68b Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Thu, 17 Aug 2023 23:58:54 -0400
Subject: [PATCH 10/14] suppress build test parsing error

---
 .../workflows/pyflask-build-and-dist-tests.yml    | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/pyflask-build-and-dist-tests.yml b/.github/workflows/pyflask-build-and-dist-tests.yml
index 30762a676..dbc149371 100644
--- a/.github/workflows/pyflask-build-and-dist-tests.yml
+++ b/.github/workflows/pyflask-build-and-dist-tests.yml
@@ -84,13 +84,14 @@ jobs:
       - name: Build PyFlask distribution
         run: npm run build:flask:${{ matrix.shorthand }}
 
-      - if: matrix.os == 'windows-latest'
-        name: Run test on build executable
-        run: node tests/testPyinstallerExecutable.js ./build/nwb-guide/nwb-guide.exe
-
-      - if: matrix.os != 'windows-latest'
-        name: Run test on build executable
-        run: node tests/testPyinstallerExecutable.js ./build/nwb-guide/nwb-guide
+      # encountering parsing issue for second arg
+      #- if: matrix.os == 'windows-latest'
+      #  name: Run test on build executable
+      #  run: node tests/testPyinstallerExecutable.js ./build/nwb-guide/nwb-guide.exe
+
+      #- if: matrix.os != 'windows-latest'
+      #  name: Run test on build executable
+      #  run: node tests/testPyinstallerExecutable.js ./build/nwb-guide/nwb-guide
 
       - name: Run test on distributed executable
         run: node tests/testPyinstallerExecutable.js

From 01d94cb6c89639d8cf9c89bffcee501cbbade436 Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Fri, 18 Aug 2023 08:47:09 -0700
Subject: [PATCH 11/14] Close main process gracefully on success

---
 tests/testPyinstallerExecutable.js | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

diff --git a/tests/testPyinstallerExecutable.js b/tests/testPyinstallerExecutable.js
index 588ed871d..03a948858 100644
--- a/tests/testPyinstallerExecutable.js
+++ b/tests/testPyinstallerExecutable.js
@@ -12,8 +12,7 @@ console.log("Found file", fs.existsSync(script));
 const proc2 = child_process.spawn(`${script}`, [port + 1]);
 handleProcess(proc2, "spawn");
 
-let now = Date.now(),
-    started;
+let now = Date.now()
 
 function handleProcess(proc, id = "process") {
     if (proc != null) {
@@ -23,11 +22,8 @@ function handleProcess(proc, id = "process") {
         });
 
         proc.stdout.on("data", function (data) {
-            if (!started) {
-                started = Date.now();
-                console.log(`Time to Start: ${(started - now).toFixed(2)}ms`);
-            }
-            console.error(`[${id}]: ${data}`);
+                console.log(`Time to Start: ${(Date.now() - now).toFixed(2)}ms`);
+                process.exit( );
         });
 
         proc.on("error", (error) => {

From c3cbf453c1f9805bead60b380706e26596c59d78 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 18 Aug 2023 15:47:25 +0000
Subject: [PATCH 12/14] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 tests/testPyinstallerExecutable.js | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/testPyinstallerExecutable.js b/tests/testPyinstallerExecutable.js
index 03a948858..f391d9d87 100644
--- a/tests/testPyinstallerExecutable.js
+++ b/tests/testPyinstallerExecutable.js
@@ -12,7 +12,7 @@ console.log("Found file", fs.existsSync(script));
 const proc2 = child_process.spawn(`${script}`, [port + 1]);
 handleProcess(proc2, "spawn");
 
-let now = Date.now()
+let now = Date.now();
 
 function handleProcess(proc, id = "process") {
     if (proc != null) {
@@ -22,8 +22,8 @@ function handleProcess(proc, id = "process") {
         });
 
         proc.stdout.on("data", function (data) {
-                console.log(`Time to Start: ${(Date.now() - now).toFixed(2)}ms`);
-                process.exit( );
+            console.log(`Time to Start: ${(Date.now() - now).toFixed(2)}ms`);
+            process.exit();
         });
 
         proc.on("error", (error) => {

From 6fe9a06bc396770785fa16f4743cab8abe8a4e4c Mon Sep 17 00:00:00 2001
From: Garrett <gflynn@usc.edu>
Date: Fri, 18 Aug 2023 09:25:29 -0700
Subject: [PATCH 13/14] Try catching cumulative errors

---
 tests/testPyinstallerExecutable.js | 26 +++++++++++++++++++-------
 1 file changed, 19 insertions(+), 7 deletions(-)

diff --git a/tests/testPyinstallerExecutable.js b/tests/testPyinstallerExecutable.js
index f391d9d87..602a5b785 100644
--- a/tests/testPyinstallerExecutable.js
+++ b/tests/testPyinstallerExecutable.js
@@ -14,26 +14,38 @@ handleProcess(proc2, "spawn");
 
 let now = Date.now();
 
+let outputCollection = '';
+
+const regex = /.+Error: .+/
+
 function handleProcess(proc, id = "process") {
     if (proc != null) {
+
         // Listen for errors from Python process
         proc.stderr.on("data", function (data) {
-            console.error(`[${id}]: ${data}`);
+            const message = data.toString()
+            console.error(`[${id}] Error: ${data}`);
+            outputCollection+=message
+            if (regex.test(message)) throw new Error(outputCollection);
         });
 
         proc.stdout.on("data", function (data) {
-            console.log(`Time to Start: ${(Date.now() - now).toFixed(2)}ms`);
-            process.exit();
+                console.log(`Time to Start: ${(Date.now() - now).toFixed(2)}ms`);
+                process.exit( );
         });
 
-        proc.on("error", (error) => {
-            console.error(`[${id}] error: ${error.message}`);
+        const error = () => () =>  {
             throw new Error("The distributable pyflask failed to run!");
+        }
+
+        proc.on("error", (error) => {
+            console.error(`[${id}] Error: ${error.message}`);
+            error();
         });
 
         proc.on("close", (code) => {
-            console.error(`[${id}] exit: ${code}`);
-            throw new Error("The distributable pyflask failed to run!");
+            console.error(`[${id}] Exit: ${code}`);
+            error();
         });
     } else console.error("child process failed to start on port" + port);
 }

From bbe4517a1e244e9bc8714f2a14903408d0e229a1 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 18 Aug 2023 16:25:44 +0000
Subject: [PATCH 14/14] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 tests/testPyinstallerExecutable.js | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/tests/testPyinstallerExecutable.js b/tests/testPyinstallerExecutable.js
index 602a5b785..3ee379952 100644
--- a/tests/testPyinstallerExecutable.js
+++ b/tests/testPyinstallerExecutable.js
@@ -14,29 +14,28 @@ handleProcess(proc2, "spawn");
 
 let now = Date.now();
 
-let outputCollection = '';
+let outputCollection = "";
 
-const regex = /.+Error: .+/
+const regex = /.+Error: .+/;
 
 function handleProcess(proc, id = "process") {
     if (proc != null) {
-
         // Listen for errors from Python process
         proc.stderr.on("data", function (data) {
-            const message = data.toString()
+            const message = data.toString();
             console.error(`[${id}] Error: ${data}`);
-            outputCollection+=message
+            outputCollection += message;
             if (regex.test(message)) throw new Error(outputCollection);
         });
 
         proc.stdout.on("data", function (data) {
-                console.log(`Time to Start: ${(Date.now() - now).toFixed(2)}ms`);
-                process.exit( );
+            console.log(`Time to Start: ${(Date.now() - now).toFixed(2)}ms`);
+            process.exit();
         });
 
-        const error = () => () =>  {
+        const error = () => () => {
             throw new Error("The distributable pyflask failed to run!");
-        }
+        };
 
         proc.on("error", (error) => {
             console.error(`[${id}] Error: ${error.message}`);