From 8f9f9f7e4a9fd5c43a97c0b3058d8ad87fa8c7b9 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Sat, 9 Sep 2023 12:19:09 +0200
Subject: [PATCH 01/24] Testing

---
 environments/environment-MAC.yml | 11 +++++------
 package.json                     |  2 +-
 2 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/environments/environment-MAC.yml b/environments/environment-MAC.yml
index cd76d4596..58c1a6855 100644
--- a/environments/environment-MAC.yml
+++ b/environments/environment-MAC.yml
@@ -1,11 +1,11 @@
 name: nwb-guide
 channels:
-  - defaults
   - conda-forge
+  - defaults
 dependencies:
-  - python = 3.9.17
-  - nodejs = 18.16.1
+  - python = 3.9.18
   - PyInstaller = 5.13.0
+  - nodejs = 18.16.1
   - numcodecs = 0.11.0
   - jsonschema = 4.18.0  # this installs jsonschema-specifications which is needed for validation
   - pydantic[email] = 2.0.2  # email validator is used by dandi
@@ -14,9 +14,8 @@ dependencies:
       - chardet == 5.1.0
       - configparser == 6.0.0
       - flask == 2.3.2
-      - flask-cors === 3.0.10
+      - flask-cors == 4.0.0
       - flask_restx == 1.1.0
       - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full]
-      - hdmf >= 3.7.0
-      - pytest == 7.2.2
+      - pytest == 7.4.0
       - pytest-cov == 4.1.0
diff --git a/package.json b/package.json
index bad2cfe3e..90c229d6e 100644
--- a/package.json
+++ b/package.json
@@ -15,7 +15,7 @@
     "build:win": "npm run build && npm run build:flask:win && npm run build:electron:win",
     "build:mac": "npm run build && npm run build:flask:unix && npm run build:electron:mac",
     "build:linux": "npm run build && npm run build:flask:unix && npm run build:electron:linux",
-    "build:flask:base": "python -m PyInstaller --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils",
+    "build:flask:base": "python -m PyInstaller --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --collect-all sonpy --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils",
     "build:flask:win": "npm run build:flask:base -- --add-data ./paths.config.json;. --add-data ./package.json;.",
     "build:flask:unix": "npm run build:flask:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --collect-all ndx_dandi_icephys",
     "build:electron:win": "electron-builder build --win --publish never",

From f49184dbf9584f2d98052df6adea4e41dd183805 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Sat, 9 Sep 2023 18:31:38 +0200
Subject: [PATCH 02/24] Set pyinstaller log level to debug

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

diff --git a/package.json b/package.json
index 90c229d6e..3838c86fb 100644
--- a/package.json
+++ b/package.json
@@ -15,7 +15,7 @@
     "build:win": "npm run build && npm run build:flask:win && npm run build:electron:win",
     "build:mac": "npm run build && npm run build:flask:unix && npm run build:electron:mac",
     "build:linux": "npm run build && npm run build:flask:unix && npm run build:electron:linux",
-    "build:flask:base": "python -m PyInstaller --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --collect-all sonpy --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils",
+    "build:flask:base": "python -m PyInstaller --log-level DEBUG --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --collect-all sonpy --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils",
     "build:flask:win": "npm run build:flask:base -- --add-data ./paths.config.json;. --add-data ./package.json;.",
     "build:flask:unix": "npm run build:flask:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --collect-all ndx_dandi_icephys",
     "build:electron:win": "electron-builder build --win --publish never",

From 7005c4bf3215c5926e03c3d73715476aa96e2185 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Sat, 9 Sep 2023 18:55:07 +0200
Subject: [PATCH 03/24] Add sonpy.so explicitly

---
 package.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index 3838c86fb..1564ef8bb 100644
--- a/package.json
+++ b/package.json
@@ -15,9 +15,9 @@
     "build:win": "npm run build && npm run build:flask:win && npm run build:electron:win",
     "build:mac": "npm run build && npm run build:flask:unix && npm run build:electron:mac",
     "build:linux": "npm run build && npm run build:flask:unix && npm run build:electron:linux",
-    "build:flask:base": "python -m PyInstaller --log-level DEBUG --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --collect-all sonpy --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils",
+    "build:flask:base": "python -m PyInstaller --log-level DEBUG --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils",
     "build:flask:win": "npm run build:flask:base -- --add-data ./paths.config.json;. --add-data ./package.json;.",
-    "build:flask:unix": "npm run build:flask:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --collect-all ndx_dandi_icephys",
+    "build:flask:unix": "npm run build:flask:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --add-data /Users/rly/mambaforge/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so:. --collect-all ndx_dandi_icephys",
     "build:electron:win": "electron-builder build --win --publish never",
     "build:electron:mac": "electron-builder build --mac --publish never",
     "build:electron:linux": "electron-builder build --linux --publish never",

From 5ead0115b34ff768e35ab3ab42440243d716b634 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Sat, 9 Sep 2023 19:52:56 +0200
Subject: [PATCH 04/24] Testing

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

diff --git a/package.json b/package.json
index 1564ef8bb..da33c69cb 100644
--- a/package.json
+++ b/package.json
@@ -17,7 +17,7 @@
     "build:linux": "npm run build && npm run build:flask:unix && npm run build:electron:linux",
     "build:flask:base": "python -m PyInstaller --log-level DEBUG --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils",
     "build:flask:win": "npm run build:flask:base -- --add-data ./paths.config.json;. --add-data ./package.json;.",
-    "build:flask:unix": "npm run build:flask:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --add-data /Users/rly/mambaforge/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so:. --collect-all ndx_dandi_icephys",
+    "build:flask:unix": "npm run build:flask:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --add-data /Users/runner/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so:. --collect-all ndx_dandi_icephys",
     "build:electron:win": "electron-builder build --win --publish never",
     "build:electron:mac": "electron-builder build --mac --publish never",
     "build:electron:linux": "electron-builder build --linux --publish never",

From 0d346cfe8302177645df1200700fdc9d112b3704 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Sat, 9 Sep 2023 20:14:55 +0200
Subject: [PATCH 05/24] Testing

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

diff --git a/package.json b/package.json
index da33c69cb..5a54117b3 100644
--- a/package.json
+++ b/package.json
@@ -17,7 +17,7 @@
     "build:linux": "npm run build && npm run build:flask:unix && npm run build:electron:linux",
     "build:flask:base": "python -m PyInstaller --log-level DEBUG --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils",
     "build:flask:win": "npm run build:flask:base -- --add-data ./paths.config.json;. --add-data ./package.json;.",
-    "build:flask:unix": "npm run build:flask:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --add-data /Users/runner/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so:. --collect-all ndx_dandi_icephys",
+    "build:flask:unix": "npm run build:flask:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --add-binary /Users/runner/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so:. --collect-all ndx_dandi_icephys",
     "build:electron:win": "electron-builder build --win --publish never",
     "build:electron:mac": "electron-builder build --mac --publish never",
     "build:electron:linux": "electron-builder build --linux --publish never",

From 53e62b26330af3e5a3fa5eefae1552b7e16a9717 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Sat, 9 Sep 2023 20:49:49 +0200
Subject: [PATCH 06/24] Testing

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

diff --git a/package.json b/package.json
index 5a54117b3..c55b82cc3 100644
--- a/package.json
+++ b/package.json
@@ -17,7 +17,7 @@
     "build:linux": "npm run build && npm run build:flask:unix && npm run build:electron:linux",
     "build:flask:base": "python -m PyInstaller --log-level DEBUG --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils",
     "build:flask:win": "npm run build:flask:base -- --add-data ./paths.config.json;. --add-data ./package.json;.",
-    "build:flask:unix": "npm run build:flask:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --add-binary /Users/runner/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so:. --collect-all ndx_dandi_icephys",
+    "build:flask:unix": "rm /Users/runner/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so && npm run build:flask:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --add-binary /Users/runner/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so:. --collect-all ndx_dandi_icephys",
     "build:electron:win": "electron-builder build --win --publish never",
     "build:electron:mac": "electron-builder build --mac --publish never",
     "build:electron:linux": "electron-builder build --linux --publish never",

From e55b823a40c6902ba9f199e5cdf87087f327182d Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Sat, 9 Sep 2023 20:50:13 +0200
Subject: [PATCH 07/24] Testing

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

diff --git a/package.json b/package.json
index c55b82cc3..6edc0071a 100644
--- a/package.json
+++ b/package.json
@@ -17,7 +17,7 @@
     "build:linux": "npm run build && npm run build:flask:unix && npm run build:electron:linux",
     "build:flask:base": "python -m PyInstaller --log-level DEBUG --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils",
     "build:flask:win": "npm run build:flask:base -- --add-data ./paths.config.json;. --add-data ./package.json;.",
-    "build:flask:unix": "rm /Users/runner/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so && npm run build:flask:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --add-binary /Users/runner/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so:. --collect-all ndx_dandi_icephys",
+    "build:flask:unix": "rm /Users/runner/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so && npm run build:flask:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --collect-all ndx_dandi_icephys",
     "build:electron:win": "electron-builder build --win --publish never",
     "build:electron:mac": "electron-builder build --mac --publish never",
     "build:electron:linux": "electron-builder build --linux --publish never",

From 499dc92f43c70551f205f9a0536ca9e850f7cff0 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Sat, 9 Sep 2023 21:16:26 +0200
Subject: [PATCH 08/24] Fix

---
 environments/environment-Windows.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/environments/environment-Windows.yml b/environments/environment-Windows.yml
index 7faeba0ee..eb846dee2 100644
--- a/environments/environment-Windows.yml
+++ b/environments/environment-Windows.yml
@@ -20,3 +20,4 @@ dependencies:
       - hdmf >= 3.7.0
       - pytest == 7.2.2
       - pytest-cov == 4.1.0
+      - email-validator == 2.0.0

From 074c2a6220855e99a08d42791796b62eae70a255 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Sat, 9 Sep 2023 21:28:55 +0200
Subject: [PATCH 09/24] Fix

---
 package.json | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/package.json b/package.json
index 6edc0071a..08db3502b 100644
--- a/package.json
+++ b/package.json
@@ -13,18 +13,19 @@
     "build": "npm run build:app",
     "build:app": "electron-vite build --outDir build",
     "build:win": "npm run build && npm run build:flask:win && npm run build:electron:win",
-    "build:mac": "npm run build && npm run build:flask:unix && npm run build:electron:mac",
+    "build:mac": "npm run build && rm /Users/runner/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so && npm run build:flask:unix && npm run build:electron:mac",
     "build:linux": "npm run build && npm run build:flask:unix && npm run build:electron:linux",
-    "build:flask:base": "python -m PyInstaller --log-level DEBUG --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils",
+    "build:flask:base": "python -m PyInstaller --log-level DEBUG --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --collect-all ndx_dandi_icephys --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils",
     "build:flask:win": "npm run build:flask:base -- --add-data ./paths.config.json;. --add-data ./package.json;.",
-    "build:flask:unix": "rm /Users/runner/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so && npm run build:flask:base -- --add-data ./paths.config.json:. --add-data ./package.json:. --collect-all ndx_dandi_icephys",
+    "build:flask:unix": "npm run build:flask:base -- --add-data ./paths.config.json:. --add-data ./package.json:.",
     "build:electron:win": "electron-builder build --win --publish never",
     "build:electron:mac": "electron-builder build --mac --publish never",
     "build:electron:linux": "electron-builder build --linux --publish never",
     "test": "npm run test:app && npm run test:server",
     "test:app": "vitest run",
     "test:server": "pytest pyflask/tests/ -s",
-    "test:executable": "concurrently -n EXE,TEST --kill-others \"node tests/testPyinstallerExecutable.js --port 3434 --forever\" \"pytest pyflask/tests/ -s --target http://localhost:3434\"",
+    "wait3s": "node -e \"setTimeout(() => process.exit(0),3000)\"",
+    "test:executable": "concurrently -n EXE,TEST --kill-others --success first \"node tests/testPyinstallerExecutable.js --port 3434 --forever\" \"npm run wait3s && pytest pyflask/tests/ -s --target http://localhost:3434\"",
     "test:coverage": "npm run coverage:app && npm run coverage:server",
     "coverage:app": "vitest run --coverage",
     "coverage:server": "pytest pyflask/tests/ -s --cov=pyflask --cov-report=xml",

From e29e43e9c8203214d7a2dcf46e3433e4742ae610 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Sat, 9 Sep 2023 21:29:18 +0200
Subject: [PATCH 10/24] Update arm64 env

---
 environments/environment-MAC-arm64.yml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/environments/environment-MAC-arm64.yml b/environments/environment-MAC-arm64.yml
index 4c0ca3ae3..20d6619d4 100644
--- a/environments/environment-MAC-arm64.yml
+++ b/environments/environment-MAC-arm64.yml
@@ -3,21 +3,22 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python = 3.9.17
+  - python = 3.9.18
   - PyInstaller = 5.13.0
   - nodejs = 18.16.1
   - numcodecs = 0.11.0
-  - lxml = 4.9.3  # pypi build fails due to x64/arm64 mismatch so install from conda-forge
-  - pyedflib = 0.1.32  # pypi build fails due to x64/arm64 mismatch so install from conda-forge
   - jsonschema = 4.18.0  # this installs jsonschema-specifications which is needed for validation
   - pydantic[email] = 2.0.2  # email validator is used by dandi
+  - lxml = 4.9.3  # pypi build fails due to x64/arm64 mismatch so install from conda-forge
+  - pyedflib = 0.1.32  # pypi build fails due to x64/arm64 mismatch so install from conda-forge
   - numpy  # may have x64/arm64 mismatch issues so install from conda-forge
   - pip
   - pip:
       - chardet == 5.1.0
       - configparser == 6.0.0
       - flask == 2.3.2
-      - flask_restx == 1.1.0
       - flask-cors == 4.0.0
+      - flask_restx == 1.1.0
       - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[ecephys]
       - pytest == 7.4.0
+      - pytest-cov == 4.1.0

From d1be94ad225f4e16164021bbc5e85715fc08f320 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Sat, 9 Sep 2023 22:02:04 +0200
Subject: [PATCH 11/24] Adjust all envs

---
 .../pyflask-build-and-dist-tests.yml          |  4 ++
 environments/environment-Linux.yml            | 37 +++++++------------
 environments/environment-MAC-arm64.yml        |  5 ++-
 environments/environment-MAC.yml              |  5 ++-
 environments/environment-Windows.yml          | 21 ++++++-----
 package.json                                  |  2 +-
 6 files changed, 36 insertions(+), 38 deletions(-)

diff --git a/.github/workflows/pyflask-build-and-dist-tests.yml b/.github/workflows/pyflask-build-and-dist-tests.yml
index e2e983010..8bf667130 100644
--- a/.github/workflows/pyflask-build-and-dist-tests.yml
+++ b/.github/workflows/pyflask-build-and-dist-tests.yml
@@ -83,6 +83,10 @@ jobs:
 
       - run: npm ci
 
+      # fix for macos build
+      - if: matrix.os == 'macos-latest'
+        run: rm /Users/runner/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so
+
       - name: Build PyFlask distribution
         run: npm run build:flask:${{ matrix.shorthand }}
 
diff --git a/environments/environment-Linux.yml b/environments/environment-Linux.yml
index 87a4fe4a1..d55ea40bf 100644
--- a/environments/environment-Linux.yml
+++ b/environments/environment-Linux.yml
@@ -1,31 +1,22 @@
 name: nwb-guide
 channels:
-  - defaults
   - conda-forge
+  - defaults
 dependencies:
-  - python = 3.9.17
-  - PyInstaller = 4.7
-  - nodejs = 16.14.2
-  - libgcc = 7.2.0
-  - git = 2.20.1
+  - python = 3.9.18
+  - PyInstaller = 5.13.0
+  - nodejs = 18.16.1
+  - numcodecs = 0.11.0
+  # install these from conda-forge so that dependent packages get included in the distributable
+  - jsonschema = 4.18.0  # installs jsonschema-specifications
+  - pydantic[email] = 2.0.2  # installs email-validator
   - pip
   - pip:
-      - chardet == 4.0.0
-      - pandas == 1.4.2
-      - openpyxl == 3.0.3
-      - pennsieve == 6.1.2
-      - configparser == 4.0.2
-      - python-docx == 0.8.10
-      - xlrd == 1.2.0
-      - biopython == 1.79
-      - flask == 2.0.2
-      - flask_restx
-      - protobuf == 3.20.0
-      - gevent == 21.12.0
-      - werkzeug == 2.0.2
-      - opencv-python == 4.5.3.56
+      - chardet == 5.1.0
+      - configparser == 6.0.0
+      - flask == 2.3.2
+      - flask-cors == 4.0.0
+      - flask_restx == 1.1.0
       - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full]
-      - hdmf >= 3.7.0
-      - pytest == 7.2.2
+      - pytest == 7.4.0
       - pytest-cov == 4.1.0
-      - flask-cors === 3.0.10
diff --git a/environments/environment-MAC-arm64.yml b/environments/environment-MAC-arm64.yml
index 20d6619d4..bb11633f9 100644
--- a/environments/environment-MAC-arm64.yml
+++ b/environments/environment-MAC-arm64.yml
@@ -7,11 +7,12 @@ dependencies:
   - PyInstaller = 5.13.0
   - nodejs = 18.16.1
   - numcodecs = 0.11.0
-  - jsonschema = 4.18.0  # this installs jsonschema-specifications which is needed for validation
-  - pydantic[email] = 2.0.2  # email validator is used by dandi
   - lxml = 4.9.3  # pypi build fails due to x64/arm64 mismatch so install from conda-forge
   - pyedflib = 0.1.32  # pypi build fails due to x64/arm64 mismatch so install from conda-forge
   - numpy  # may have x64/arm64 mismatch issues so install from conda-forge
+  # install these from conda-forge so that dependent packages get included in the distributable
+  - jsonschema = 4.18.0  # installs jsonschema-specifications
+  - pydantic[email] = 2.0.2  # installs email-validator
   - pip
   - pip:
       - chardet == 5.1.0
diff --git a/environments/environment-MAC.yml b/environments/environment-MAC.yml
index 58c1a6855..d55ea40bf 100644
--- a/environments/environment-MAC.yml
+++ b/environments/environment-MAC.yml
@@ -7,8 +7,9 @@ dependencies:
   - PyInstaller = 5.13.0
   - nodejs = 18.16.1
   - numcodecs = 0.11.0
-  - jsonschema = 4.18.0  # this installs jsonschema-specifications which is needed for validation
-  - pydantic[email] = 2.0.2  # email validator is used by dandi
+  # install these from conda-forge so that dependent packages get included in the distributable
+  - jsonschema = 4.18.0  # installs jsonschema-specifications
+  - pydantic[email] = 2.0.2  # installs email-validator
   - pip
   - pip:
       - chardet == 5.1.0
diff --git a/environments/environment-Windows.yml b/environments/environment-Windows.yml
index eb846dee2..6a53b6567 100644
--- a/environments/environment-Windows.yml
+++ b/environments/environment-Windows.yml
@@ -1,23 +1,24 @@
 name: nwb-guide
 channels:
-  - defaults
   - conda-forge
+  - defaults
 dependencies:
-  - python = 3.9.17
-  - nodejs = 18.16.1
+  - python = 3.9.18
   - PyInstaller = 5.13.0
-  - pywin32 = 303
-  - git = 2.20.1
-  - setuptools=58.0.4
+  - nodejs = 18.16.1
+  - numcodecs = 0.11.0  # not sure if this is needed
+  - pywin32 = 303  # not sure if this is needed
+  # install these from conda-forge so that dependent packages get included in the distributable
+  - jsonschema = 4.18.0  # installs jsonschema-specifications
+  - pydantic[email] = 2.0.2  # installs email-validator
   - pip
   - pip:
       - chardet == 5.1.0
       - configparser == 6.0.0
       - flask == 2.3.2
-      - flask-cors === 3.0.10
+      - flask-cors == 4.0.0
       - flask_restx == 1.1.0
       - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full]
-      - hdmf >= 3.7.0
-      - pytest == 7.2.2
+      - pytest == 7.4.0
       - pytest-cov == 4.1.0
-      - email-validator == 2.0.0
+
diff --git a/package.json b/package.json
index 08db3502b..f9aff8eab 100644
--- a/package.json
+++ b/package.json
@@ -13,7 +13,7 @@
     "build": "npm run build:app",
     "build:app": "electron-vite build --outDir build",
     "build:win": "npm run build && npm run build:flask:win && npm run build:electron:win",
-    "build:mac": "npm run build && rm /Users/runner/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so && npm run build:flask:unix && npm run build:electron:mac",
+    "build:mac": "npm run build && npm run build:flask:unix && npm run build:electron:mac",
     "build:linux": "npm run build && npm run build:flask:unix && npm run build:electron:linux",
     "build:flask:base": "python -m PyInstaller --log-level DEBUG --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --collect-all ndx_dandi_icephys --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils",
     "build:flask:win": "npm run build:flask:base -- --add-data ./paths.config.json;. --add-data ./package.json;.",

From 18c363ce6563d68b2ca5dfa1c905d54ef29cbec8 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 9 Sep 2023 20:02:22 +0000
Subject: [PATCH 12/24] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 environments/environment-Windows.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/environments/environment-Windows.yml b/environments/environment-Windows.yml
index 6a53b6567..5783d3f9b 100644
--- a/environments/environment-Windows.yml
+++ b/environments/environment-Windows.yml
@@ -21,4 +21,3 @@ dependencies:
       - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full]
       - pytest == 7.4.0
       - pytest-cov == 4.1.0
-

From 0760fc4d2ce8d9b3a515b90ac5d04f25f50899e2 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Sat, 9 Sep 2023 22:38:12 +0200
Subject: [PATCH 13/24] Fix windows?

---
 environments/environment-Windows.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/environments/environment-Windows.yml b/environments/environment-Windows.yml
index 5783d3f9b..6e8bf2815 100644
--- a/environments/environment-Windows.yml
+++ b/environments/environment-Windows.yml
@@ -19,5 +19,6 @@ dependencies:
       - flask-cors == 4.0.0
       - flask_restx == 1.1.0
       - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full]
+      - hdmf >= 3.7.0
       - pytest == 7.4.0
       - pytest-cov == 4.1.0

From cd9e512dc1ea172ff31b9171609151510b3aadc0 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Sat, 9 Sep 2023 22:56:10 +0200
Subject: [PATCH 14/24] Fix mac build from cache

---
 .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 8bf667130..5fbea858d 100644
--- a/.github/workflows/pyflask-build-and-dist-tests.yml
+++ b/.github/workflows/pyflask-build-and-dist-tests.yml
@@ -85,7 +85,7 @@ jobs:
 
       # fix for macos build
       - if: matrix.os == 'macos-latest'
-        run: rm /Users/runner/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so
+        run: rm -f /Users/runner/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so
 
       - name: Build PyFlask distribution
         run: npm run build:flask:${{ matrix.shorthand }}

From 7f1d4d6474cfa068b1ed6523345e02ed2992e9a0 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Sat, 9 Sep 2023 22:56:14 +0200
Subject: [PATCH 15/24] reset windows

---
 environments/environment-Windows.yml | 43 ++++++++++++++++++++++------
 1 file changed, 34 insertions(+), 9 deletions(-)

diff --git a/environments/environment-Windows.yml b/environments/environment-Windows.yml
index 6e8bf2815..9030ad6b0 100644
--- a/environments/environment-Windows.yml
+++ b/environments/environment-Windows.yml
@@ -1,24 +1,49 @@
 name: nwb-guide
 channels:
-  - conda-forge
   - defaults
+  - conda-forge
 dependencies:
-  - python = 3.9.18
-  - PyInstaller = 5.13.0
+  - python = 3.9.17
   - nodejs = 18.16.1
-  - numcodecs = 0.11.0  # not sure if this is needed
-  - pywin32 = 303  # not sure if this is needed
-  # install these from conda-forge so that dependent packages get included in the distributable
-  - jsonschema = 4.18.0  # installs jsonschema-specifications
+  - PyInstaller = 5.13.0
+  - pywin32 = 303
+  - git = 2.20.1
+  - setuptools=58.0.4
   - pydantic[email] = 2.0.2  # installs email-validator
   - pip
   - pip:
       - chardet == 5.1.0
       - configparser == 6.0.0
       - flask == 2.3.2
-      - flask-cors == 4.0.0
+      - flask-cors === 3.0.10
       - flask_restx == 1.1.0
       - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full]
       - hdmf >= 3.7.0
-      - pytest == 7.4.0
+      - pytest == 7.2.2
       - pytest-cov == 4.1.0
+      # - email-validator == 2.0.0
+
+# name: nwb-guide
+# channels:
+#   - conda-forge
+#   - defaults
+# dependencies:
+#   - python = 3.9.18
+#   - PyInstaller = 5.13.0
+#   - nodejs = 18.16.1
+#   - numcodecs = 0.11.0  # not sure if this is needed
+#   - pywin32 = 303  # not sure if this is needed
+#   # install these from conda-forge so that dependent packages get included in the distributable
+#   - jsonschema = 4.18.0  # installs jsonschema-specifications
+#   - pydantic[email] = 2.0.2  # installs email-validator
+#   - pip
+#   - pip:
+#       - chardet == 5.1.0
+#       - configparser == 6.0.0
+#       - flask == 2.3.2
+#       - flask-cors == 4.0.0
+#       - flask_restx == 1.1.0
+#       - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full]
+#       - hdmf >= 3.7.0
+#       - pytest == 7.4.0
+#       - pytest-cov == 4.1.0

From 0a5d9d0db7eed16efc4d4a1c3fb65cad59687a41 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Sat, 9 Sep 2023 23:30:43 +0200
Subject: [PATCH 16/24] reset windows

---
 environments/environment-Windows.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/environments/environment-Windows.yml b/environments/environment-Windows.yml
index 9030ad6b0..44ef46d0c 100644
--- a/environments/environment-Windows.yml
+++ b/environments/environment-Windows.yml
@@ -9,7 +9,6 @@ dependencies:
   - pywin32 = 303
   - git = 2.20.1
   - setuptools=58.0.4
-  - pydantic[email] = 2.0.2  # installs email-validator
   - pip
   - pip:
       - chardet == 5.1.0
@@ -21,7 +20,7 @@ dependencies:
       - hdmf >= 3.7.0
       - pytest == 7.2.2
       - pytest-cov == 4.1.0
-      # - email-validator == 2.0.0
+      - email-validator == 2.0.0
 
 # name: nwb-guide
 # channels:

From 92e1f4653ce298542e62b2139024c7a9a31ea032 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Sat, 9 Sep 2023 23:47:22 +0200
Subject: [PATCH 17/24] Fix missing import

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

diff --git a/package.json b/package.json
index f9aff8eab..7bfa42d93 100644
--- a/package.json
+++ b/package.json
@@ -15,7 +15,7 @@
     "build:win": "npm run build && npm run build:flask:win && npm run build:electron:win",
     "build:mac": "npm run build && npm run build:flask:unix && npm run build:electron:mac",
     "build:linux": "npm run build && npm run build:flask:unix && npm run build:electron:linux",
-    "build:flask:base": "python -m PyInstaller --log-level DEBUG --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --collect-all ndx_dandi_icephys --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils",
+    "build:flask:base": "python -m PyInstaller --log-level DEBUG --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --collect-all ndx_dandi_icephys --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils --hidden-import email_validator",
     "build:flask:win": "npm run build:flask:base -- --add-data ./paths.config.json;. --add-data ./package.json;.",
     "build:flask:unix": "npm run build:flask:base -- --add-data ./paths.config.json:. --add-data ./package.json:.",
     "build:electron:win": "electron-builder build --win --publish never",

From 9b84832a524e99a6b38b2a7a18eb110046f5f0be Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 12 Sep 2023 12:30:08 -0400
Subject: [PATCH 18/24] try neuroconv specific debug

---
 environments/environment-MAC-arm64.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environments/environment-MAC-arm64.yml b/environments/environment-MAC-arm64.yml
index bb11633f9..93bd9ef53 100644
--- a/environments/environment-MAC-arm64.yml
+++ b/environments/environment-MAC-arm64.yml
@@ -20,6 +20,6 @@ dependencies:
       - flask == 2.3.2
       - flask-cors == 4.0.0
       - flask_restx == 1.1.0
-      - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[ecephys]
+      - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@improve_sonpy_installation_m1#neuroconv[full]
       - pytest == 7.4.0
       - pytest-cov == 4.1.0

From c3658e7bf71d7a2ca6545a11161c39f9cd23bedd Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 12 Sep 2023 13:45:44 -0400
Subject: [PATCH 19/24] Update pyflask-build-and-dist-tests.yml

---
 .github/workflows/pyflask-build-and-dist-tests.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pyflask-build-and-dist-tests.yml b/.github/workflows/pyflask-build-and-dist-tests.yml
index 5fbea858d..a58c77944 100644
--- a/.github/workflows/pyflask-build-and-dist-tests.yml
+++ b/.github/workflows/pyflask-build-and-dist-tests.yml
@@ -85,7 +85,9 @@ jobs:
 
       # fix for macos build
       - if: matrix.os == 'macos-latest'
-        run: rm -f /Users/runner/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so
+        run: |
+          rm -f /Users/runner/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so
+          rm -f /usr/local/miniconda/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so
 
       - name: Build PyFlask distribution
         run: npm run build:flask:${{ matrix.shorthand }}

From e3d9eff1acc6f20a561d4d6c6e74ef3401e614c3 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 12 Sep 2023 13:46:59 -0400
Subject: [PATCH 20/24] Update Build-and-deploy-mac.yml

---
 .github/workflows/Build-and-deploy-mac.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/Build-and-deploy-mac.yml b/.github/workflows/Build-and-deploy-mac.yml
index e4ee051bf..3411f2fed 100644
--- a/.github/workflows/Build-and-deploy-mac.yml
+++ b/.github/workflows/Build-and-deploy-mac.yml
@@ -33,6 +33,9 @@ jobs:
       - name: Install package.json modules and their dependencies
         run: npm install --ignore-scripts
 
+      - if: matrix.os == 'macos-latest'
+        run: rm -f /usr/local/miniconda/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so
+
       - uses: apple-actions/import-codesign-certs@v1
         with:
           # https://developer.apple.com/account/resources/certificates/add
@@ -56,5 +59,4 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           appleId: ${{ secrets.APPLE_ID }}  # currently this is set to Ryan's Apple ID and password
           appleIdPassword: ${{ secrets.APPLE_PASSWORD }}
-        run: |
-          npm run deploy:mac
+        run: npm run deploy:mac

From 97b1caa6eee66f4e1d398ea7d97e59e9c6897bc0 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 12 Sep 2023 13:47:13 -0400
Subject: [PATCH 21/24] Update pyflask-build-and-dist-tests.yml

---
 .github/workflows/pyflask-build-and-dist-tests.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/pyflask-build-and-dist-tests.yml b/.github/workflows/pyflask-build-and-dist-tests.yml
index a58c77944..5fbea858d 100644
--- a/.github/workflows/pyflask-build-and-dist-tests.yml
+++ b/.github/workflows/pyflask-build-and-dist-tests.yml
@@ -85,9 +85,7 @@ jobs:
 
       # fix for macos build
       - if: matrix.os == 'macos-latest'
-        run: |
-          rm -f /Users/runner/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so
-          rm -f /usr/local/miniconda/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so
+        run: rm -f /Users/runner/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so
 
       - name: Build PyFlask distribution
         run: npm run build:flask:${{ matrix.shorthand }}

From 97b8d8f86cc26e140272f564479372960c070aca Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 12 Sep 2023 14:08:21 -0400
Subject: [PATCH 22/24] Update Build-and-deploy-mac.yml

---
 .github/workflows/Build-and-deploy-mac.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/Build-and-deploy-mac.yml b/.github/workflows/Build-and-deploy-mac.yml
index 3411f2fed..dd7a77988 100644
--- a/.github/workflows/Build-and-deploy-mac.yml
+++ b/.github/workflows/Build-and-deploy-mac.yml
@@ -33,7 +33,7 @@ jobs:
       - name: Install package.json modules and their dependencies
         run: npm install --ignore-scripts
 
-      - if: matrix.os == 'macos-latest'
+      - name: Remove bad sonpy file (might make Spike2 format unusable on Mac - should exclude from selection)
         run: rm -f /usr/local/miniconda/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so
 
       - uses: apple-actions/import-codesign-certs@v1

From 942edbdbbf4ab441faebf59372cccfdf7abecf13 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 12 Sep 2023 14:09:15 -0400
Subject: [PATCH 23/24] update to main post merge

---
 environments/environment-MAC-arm64.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environments/environment-MAC-arm64.yml b/environments/environment-MAC-arm64.yml
index 93bd9ef53..6e4508a61 100644
--- a/environments/environment-MAC-arm64.yml
+++ b/environments/environment-MAC-arm64.yml
@@ -20,6 +20,6 @@ dependencies:
       - flask == 2.3.2
       - flask-cors == 4.0.0
       - flask_restx == 1.1.0
-      - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@improve_sonpy_installation_m1#neuroconv[full]
+      - neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main#neuroconv[full]
       - pytest == 7.4.0
       - pytest-cov == 4.1.0

From ddcbc4b255789e7a454ee432bd3fa73243c69809 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 12 Sep 2023 15:09:56 -0400
Subject: [PATCH 24/24] Update package.json

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

diff --git a/package.json b/package.json
index 7bfa42d93..3ea6741de 100644
--- a/package.json
+++ b/package.json
@@ -1,7 +1,7 @@
 {
   "name": "nwb-guide",
   "productName": "NWB GUIDE",
-  "version": "0.0.4",
+  "version": "0.0.5",
   "description": "",
   "main": "./build/main/main.js",
   "scripts": {