From e8c9297a7fc12cd6d66f94b0770bf5a30818e3c1 Mon Sep 17 00:00:00 2001
From: emjoyce <emilybemily55@gmail.com>
Date: Fri, 6 Oct 2023 11:27:07 -0700
Subject: [PATCH 01/24] clear gmsh between initializations

---
 neuron_morphology/transforms/streamline.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/neuron_morphology/transforms/streamline.py b/neuron_morphology/transforms/streamline.py
index b04d78d5..7e588c25 100644
--- a/neuron_morphology/transforms/streamline.py
+++ b/neuron_morphology/transforms/streamline.py
@@ -98,6 +98,7 @@ def generate_laplace_field(top_line: List[Tuple],
 
     # Create mesh with gmsh
     gmsh.initialize()
+    gmsh.clear()
 
     # Set up the points
     point_tags = [gmsh.model.geo.addPoint(x, y, 0, meshSize=mesh_res)

From acdad27578737c23f0151d0c0b9c3701e22e94fc Mon Sep 17 00:00:00 2001
From: gouwens <nathang@alleninstitute.org>
Date: Tue, 20 Feb 2024 12:59:21 -0800
Subject: [PATCH 02/24] Create python-package-conda.yml

---
 .github/workflows/python-package-conda.yml | 40 ++++++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 .github/workflows/python-package-conda.yml

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
new file mode 100644
index 00000000..853cdb4c
--- /dev/null
+++ b/.github/workflows/python-package-conda.yml
@@ -0,0 +1,40 @@
+name: Python Package using Conda
+
+on: [push]
+
+jobs:
+  build-windows:
+    runs-on: windows-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.9'
+        cache: 'pip'
+    - name: Add conda to system path
+      run: |
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+        echo $CONDA/bin >> $GITHUB_PATH
+    - name: Install dependencies
+      run: |
+        conda env update --file environment.yml --name base
+        conda install tqdm openjpeg ruamel.yaml
+        python -m pip install --upgrade pip
+        pip install -r test_requirements.txt -U
+        pip install -r requirements.txt -U
+        pip install .
+    - name: Lint with flake8
+      run: |
+        conda install flake8
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        conda install pytest
+        pytest tests/

From 37cc2455d8ed4c6f10a9cff4d119bcf5a6966f6c Mon Sep 17 00:00:00 2001
From: gouwens <nathang@alleninstitute.org>
Date: Tue, 20 Feb 2024 13:05:44 -0800
Subject: [PATCH 03/24] Update python-package-conda.yml

---
 .github/workflows/python-package-conda.yml | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
index 853cdb4c..2cacf859 100644
--- a/.github/workflows/python-package-conda.yml
+++ b/.github/workflows/python-package-conda.yml
@@ -15,26 +15,22 @@ jobs:
       with:
         python-version: '3.9'
         cache: 'pip'
-    - name: Add conda to system path
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
     - name: Install dependencies
       run: |
-        conda env update --file environment.yml --name base
-        conda install tqdm openjpeg ruamel.yaml
+        C:\Miniconda\condabin\conda.bat env update --file environment.yml --name base
+        C:\Miniconda\condabin\conda.bat install tqdm openjpeg ruamel.yaml
         python -m pip install --upgrade pip
         pip install -r test_requirements.txt -U
         pip install -r requirements.txt -U
         pip install .
     - name: Lint with flake8
       run: |
-        conda install flake8
+        C:\Miniconda\condabin\conda.bat install flake8
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
-        conda install pytest
+        C:\Miniconda\condabin\conda.bat install pytest
         pytest tests/

From d8a7301b249ef9a950fe9b82e7edaffdd7f57f97 Mon Sep 17 00:00:00 2001
From: gouwens <nathang@alleninstitute.org>
Date: Tue, 20 Feb 2024 13:15:35 -0800
Subject: [PATCH 04/24] Update python-package-conda.yml

---
 .github/workflows/python-package-conda.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
index 2cacf859..a40fc6a3 100644
--- a/.github/workflows/python-package-conda.yml
+++ b/.github/workflows/python-package-conda.yml
@@ -22,7 +22,6 @@ jobs:
         python -m pip install --upgrade pip
         pip install -r test_requirements.txt -U
         pip install -r requirements.txt -U
-        pip install .
     - name: Lint with flake8
       run: |
         C:\Miniconda\condabin\conda.bat install flake8
@@ -32,5 +31,4 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
-        C:\Miniconda\condabin\conda.bat install pytest
         pytest tests/

From 1439c25ce0144aea4c90ccc2311206203c1596ee Mon Sep 17 00:00:00 2001
From: gouwens <nathang@alleninstitute.org>
Date: Tue, 20 Feb 2024 13:34:57 -0800
Subject: [PATCH 05/24] Update python-package-conda.yml

---
 .github/workflows/python-package-conda.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
index a40fc6a3..8eb90087 100644
--- a/.github/workflows/python-package-conda.yml
+++ b/.github/workflows/python-package-conda.yml
@@ -22,9 +22,10 @@ jobs:
         python -m pip install --upgrade pip
         pip install -r test_requirements.txt -U
         pip install -r requirements.txt -U
+        pip install -e .
     - name: Lint with flake8
       run: |
-        C:\Miniconda\condabin\conda.bat install flake8
+        # flake8 already installed via test_requirements.txt
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide

From a7589b3476176253c3f70804478054e8fd882ef7 Mon Sep 17 00:00:00 2001
From: gouwens <nathang@alleninstitute.org>
Date: Tue, 20 Feb 2024 13:56:42 -0800
Subject: [PATCH 06/24] Update python-package-conda.yml

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

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
index 8eb90087..82cc4999 100644
--- a/.github/workflows/python-package-conda.yml
+++ b/.github/workflows/python-package-conda.yml
@@ -32,4 +32,4 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
-        pytest tests/
+        python -m pytest tests/

From 5104c3b9cb077f2829d54fabb1611470f8bc9826 Mon Sep 17 00:00:00 2001
From: gouwens <nathang@alleninstitute.org>
Date: Tue, 20 Feb 2024 13:57:56 -0800
Subject: [PATCH 07/24] Update python-package-conda.yml

---
 .github/workflows/python-package-conda.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
index 82cc4999..8a0cd1c1 100644
--- a/.github/workflows/python-package-conda.yml
+++ b/.github/workflows/python-package-conda.yml
@@ -9,9 +9,9 @@ jobs:
       max-parallel: 5
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python 3.9
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: '3.9'
         cache: 'pip'

From 879a30c726192dd9bebcdd0044cbffe3f7375a26 Mon Sep 17 00:00:00 2001
From: gouwens <nathang@alleninstitute.org>
Date: Tue, 20 Feb 2024 14:28:22 -0800
Subject: [PATCH 08/24] Update test_post_data_to_s3.py

---
 tests/pipeline/test_post_data_to_s3.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/pipeline/test_post_data_to_s3.py b/tests/pipeline/test_post_data_to_s3.py
index 07fbebc7..77ab9cb2 100644
--- a/tests/pipeline/test_post_data_to_s3.py
+++ b/tests/pipeline/test_post_data_to_s3.py
@@ -2,7 +2,7 @@
 import os
 import boto3
 import zipfile
-from moto import mock_s3
+from moto import mock_aws
 import unittest
 
 from neuron_morphology.pipeline.post_data_to_s3 import post_object_to_s3, zip_files
@@ -35,7 +35,7 @@ def test_zip_files(self):
 
         self.assertListEqual(self.mock_listing, file_list)
 
-@mock_s3
+@mock_aws
 def test_post_data_to_s3(tmpdir_factory):
     
     temp_output_dir = str(tmpdir_factory.mktemp("test"))

From 11080e10e6edadcce9a1788386b173077577aad2 Mon Sep 17 00:00:00 2001
From: gouwens <nathang@alleninstitute.org>
Date: Tue, 20 Feb 2024 14:43:11 -0800
Subject: [PATCH 09/24] Update python-package-conda.yml

Add Linux and MacOS
---
 .github/workflows/python-package-conda.yml | 50 +++++++++++++++++++++-
 1 file changed, 49 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
index 8a0cd1c1..c18306f2 100644
--- a/.github/workflows/python-package-conda.yml
+++ b/.github/workflows/python-package-conda.yml
@@ -17,12 +17,36 @@ jobs:
         cache: 'pip'
     - name: Install dependencies
       run: |
-        C:\Miniconda\condabin\conda.bat env update --file environment.yml --name base
+        C:\Miniconda\condabin\conda.bat env update --name base
         C:\Miniconda\condabin\conda.bat install tqdm openjpeg ruamel.yaml
         python -m pip install --upgrade pip
         pip install -r test_requirements.txt -U
         pip install -r requirements.txt -U
         pip install -e .
+    - name: Test with pytest
+      run: |
+        python -m pytest tests/
+  
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.9'
+        cache: 'pip'
+    - name: Install dependencies
+      run: |
+        conda env update --name base
+        conda install tqdm openjpeg ruamel.yaml
+        python -m pip install --upgrade pip
+        pip install -r test_requirements.txt -U
+        pip install -r requirements.txt -U
+        pip install -e .
     - name: Lint with flake8
       run: |
         # flake8 already installed via test_requirements.txt
@@ -33,3 +57,27 @@ jobs:
     - name: Test with pytest
       run: |
         python -m pytest tests/
+  
+  build-mac:
+    runs-on: macos-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.9'
+        cache: 'pip'
+    - name: Install dependencies
+      run: |
+        conda env update --name base
+        conda install tqdm openjpeg ruamel.yaml
+        python -m pip install --upgrade pip
+        pip install -r test_requirements.txt -U
+        pip install -r requirements.txt -U
+        pip install -e .
+    - name: Test with pytest
+      run: |
+        python -m pytest tests/

From 9e7f58492775c2fe7a0bd48dee1286465e90b1b8 Mon Sep 17 00:00:00 2001
From: gouwens <nathang@alleninstitute.org>
Date: Tue, 20 Feb 2024 14:47:28 -0800
Subject: [PATCH 10/24] Update python-package-conda.yml

---
 .github/workflows/python-package-conda.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
index c18306f2..68e27510 100644
--- a/.github/workflows/python-package-conda.yml
+++ b/.github/workflows/python-package-conda.yml
@@ -17,7 +17,6 @@ jobs:
         cache: 'pip'
     - name: Install dependencies
       run: |
-        C:\Miniconda\condabin\conda.bat env update --name base
         C:\Miniconda\condabin\conda.bat install tqdm openjpeg ruamel.yaml
         python -m pip install --upgrade pip
         pip install -r test_requirements.txt -U
@@ -41,7 +40,6 @@ jobs:
         cache: 'pip'
     - name: Install dependencies
       run: |
-        conda env update --name base
         conda install tqdm openjpeg ruamel.yaml
         python -m pip install --upgrade pip
         pip install -r test_requirements.txt -U
@@ -72,7 +70,6 @@ jobs:
         cache: 'pip'
     - name: Install dependencies
       run: |
-        conda env update --name base
         conda install tqdm openjpeg ruamel.yaml
         python -m pip install --upgrade pip
         pip install -r test_requirements.txt -U

From 59a2df5941812ade9e256daf1472ddd455adee29 Mon Sep 17 00:00:00 2001
From: gouwens <nathang@alleninstitute.org>
Date: Tue, 20 Feb 2024 14:53:42 -0800
Subject: [PATCH 11/24] Update layer_histogram.py

Fix bug with incorrect comparison operator
---
 neuron_morphology/features/layer/layer_histogram.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/neuron_morphology/features/layer/layer_histogram.py b/neuron_morphology/features/layer/layer_histogram.py
index bf2c6436..243aa262 100644
--- a/neuron_morphology/features/layer/layer_histogram.py
+++ b/neuron_morphology/features/layer/layer_histogram.py
@@ -43,7 +43,7 @@ def ensure_tuple(
         raise ValueError("if_none must be a tuple or \"raise\"")
 
     if inputs is None:
-        if if_none is "raise":
+        if if_none == "raise":
             raise ValueError("inputs were None")
         else:
             return if_none # type: ignore[]

From b07631a8e5b5d71b5d4ca2d032d16160dea10c8b Mon Sep 17 00:00:00 2001
From: gouwens <nathang@alleninstitute.org>
Date: Tue, 20 Feb 2024 14:56:29 -0800
Subject: [PATCH 12/24] Update mark.py

Fix bug (perhaps) with nonexistent type
---
 neuron_morphology/feature_extractor/mark.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/neuron_morphology/feature_extractor/mark.py b/neuron_morphology/feature_extractor/mark.py
index b2bb1114..498b7ff8 100644
--- a/neuron_morphology/feature_extractor/mark.py
+++ b/neuron_morphology/feature_extractor/mark.py
@@ -72,7 +72,7 @@ class RequiresRelativeSomaDepth(Mark):
 
     @classmethod
     def validate(cls, data: Data) -> bool:
-        return data.morphology.has_type(RELATIVE_SOMA_DEPTH)
+        return data.morphology.has_type(SOMA)
 
 class RequiresSoma(Mark):
     """Indicates that these features require a soma."""

From c460417764e5dc5ef3418f8bac05f416a5922c5a Mon Sep 17 00:00:00 2001
From: gouwens <nathang@alleninstitute.org>
Date: Mon, 29 Apr 2024 09:05:53 -0700
Subject: [PATCH 13/24] Create publish.yml

Add GitHub Action to publish to PyPI
---
 .github/workflows/publish.yml | 53 +++++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)
 create mode 100644 .github/workflows/publish.yml

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
new file mode 100644
index 00000000..71a5a19c
--- /dev/null
+++ b/.github/workflows/publish.yml
@@ -0,0 +1,53 @@
+name: Publish Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  release-build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.9"
+          cache: 'pip'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -U twine setuptools wheel
+
+      - name: build release distributions
+        run: |
+          python setup.py sdist
+          python setup.py bdist_wheel
+
+      - name: upload windows dists
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - release-build
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

From 25be1201ab261125c6ac123953c4ed8066828cda Mon Sep 17 00:00:00 2001
From: gouwens <nathang@alleninstitute.org>
Date: Mon, 29 Apr 2024 09:10:55 -0700
Subject: [PATCH 14/24] Update python-package-conda.yml

Disabling incorrect flagging of notice as error for mac build
---
 .github/workflows/python-package-conda.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
index 68e27510..e9d140c6 100644
--- a/.github/workflows/python-package-conda.yml
+++ b/.github/workflows/python-package-conda.yml
@@ -18,7 +18,7 @@ jobs:
     - name: Install dependencies
       run: |
         C:\Miniconda\condabin\conda.bat install tqdm openjpeg ruamel.yaml
-        python -m pip install --upgrade pip
+        python -m pip install --upgrade pip 
         pip install -r test_requirements.txt -U
         pip install -r requirements.txt -U
         pip install -e .
@@ -71,7 +71,7 @@ jobs:
     - name: Install dependencies
       run: |
         conda install tqdm openjpeg ruamel.yaml
-        python -m pip install --upgrade pip
+        python -m pip install --upgrade pip --disable-pip-version-check
         pip install -r test_requirements.txt -U
         pip install -r requirements.txt -U
         pip install -e .

From 71707e42c2571ab5cc3b8c87d5878e3fd2090d91 Mon Sep 17 00:00:00 2001
From: gouwens <nathang@alleninstitute.org>
Date: Mon, 29 Apr 2024 09:13:39 -0700
Subject: [PATCH 15/24] Update python-package-conda.yml

Putting the flag in the right place
---
 .github/workflows/python-package-conda.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
index e9d140c6..474b2551 100644
--- a/.github/workflows/python-package-conda.yml
+++ b/.github/workflows/python-package-conda.yml
@@ -71,10 +71,10 @@ jobs:
     - name: Install dependencies
       run: |
         conda install tqdm openjpeg ruamel.yaml
-        python -m pip install --upgrade pip --disable-pip-version-check
-        pip install -r test_requirements.txt -U
-        pip install -r requirements.txt -U
-        pip install -e .
+        python -m pip install --upgrade pip
+        pip install -r test_requirements.txt -U --disable-pip-version-check
+        pip install -r requirements.txt -U --disable-pip-version-check
+        pip install -e . --disable-pip-version-check
     - name: Test with pytest
       run: |
         python -m pytest tests/

From 0603e560ae5a8c9824bb80d38f725c76615395c9 Mon Sep 17 00:00:00 2001
From: gouwens <nathang@alleninstitute.org>
Date: Mon, 29 Apr 2024 09:23:11 -0700
Subject: [PATCH 16/24] Update python-package-conda.yml

Install conda for MacOS build since no longer provided by default
---
 .github/workflows/python-package-conda.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
index 474b2551..4a1a6788 100644
--- a/.github/workflows/python-package-conda.yml
+++ b/.github/workflows/python-package-conda.yml
@@ -68,6 +68,8 @@ jobs:
       with:
         python-version: '3.9'
         cache: 'pip'
+    - name: Set up Conda
+      uses: conda-incubator/setup-miniconda@v3
     - name: Install dependencies
       run: |
         conda install tqdm openjpeg ruamel.yaml

From 3361938dec032d88490dd8e9f5bcec6227b534a2 Mon Sep 17 00:00:00 2001
From: gouwens <nathang@alleninstitute.org>
Date: Mon, 29 Apr 2024 09:27:58 -0700
Subject: [PATCH 17/24] Update python-package-conda.yml

Adding hdf5 via conda since seems to be missing now
---
 .github/workflows/python-package-conda.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
index 4a1a6788..ea858bb3 100644
--- a/.github/workflows/python-package-conda.yml
+++ b/.github/workflows/python-package-conda.yml
@@ -72,7 +72,7 @@ jobs:
       uses: conda-incubator/setup-miniconda@v3
     - name: Install dependencies
       run: |
-        conda install tqdm openjpeg ruamel.yaml
+        conda install tqdm openjpeg ruamel.yaml h5py
         python -m pip install --upgrade pip
         pip install -r test_requirements.txt -U --disable-pip-version-check
         pip install -r requirements.txt -U --disable-pip-version-check

From 2518234d697d41862f25597f8f9a23dd8a3a22ef Mon Sep 17 00:00:00 2001
From: gouwens <nathang@alleninstitute.org>
Date: Mon, 29 Apr 2024 09:30:31 -0700
Subject: [PATCH 18/24] Update python-package-conda.yml

Trying pytables via conda for macos
---
 .github/workflows/python-package-conda.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
index ea858bb3..6f246f48 100644
--- a/.github/workflows/python-package-conda.yml
+++ b/.github/workflows/python-package-conda.yml
@@ -72,7 +72,7 @@ jobs:
       uses: conda-incubator/setup-miniconda@v3
     - name: Install dependencies
       run: |
-        conda install tqdm openjpeg ruamel.yaml h5py
+        conda install tqdm openjpeg ruamel.yaml pytables h5py
         python -m pip install --upgrade pip
         pip install -r test_requirements.txt -U --disable-pip-version-check
         pip install -r requirements.txt -U --disable-pip-version-check

From 7baf19afecd894789c7aa9fd4168297a4bffa856 Mon Sep 17 00:00:00 2001
From: gouwens <nathang@alleninstitute.org>
Date: Mon, 29 Apr 2024 09:42:56 -0700
Subject: [PATCH 19/24] Update python-package-conda.yml

Trying homebrew to get tables installed with hdf5 instead of conda
---
 .github/workflows/python-package-conda.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
index 6f246f48..afdc9328 100644
--- a/.github/workflows/python-package-conda.yml
+++ b/.github/workflows/python-package-conda.yml
@@ -72,10 +72,11 @@ jobs:
       uses: conda-incubator/setup-miniconda@v3
     - name: Install dependencies
       run: |
-        conda install tqdm openjpeg ruamel.yaml pytables h5py
+        conda install tqdm openjpeg ruamel.yaml
+        brew install hdf5
         python -m pip install --upgrade pip
         pip install -r test_requirements.txt -U --disable-pip-version-check
-        pip install -r requirements.txt -U --disable-pip-version-check
+        HDF5_DIR=/opt/homebrew/Cellar/hdf5/1.14.3 pip install -r requirements.txt -U --disable-pip-version-check
         pip install -e . --disable-pip-version-check
     - name: Test with pytest
       run: |

From 85903bc1f379fbf36d02afc121651d46cb33359a Mon Sep 17 00:00:00 2001
From: gouwens <nathang@alleninstitute.org>
Date: Mon, 29 Apr 2024 09:45:15 -0700
Subject: [PATCH 20/24] Update python-package-conda.yml

Adjusting hdf5 dir name
---
 .github/workflows/python-package-conda.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
index afdc9328..c2b792fa 100644
--- a/.github/workflows/python-package-conda.yml
+++ b/.github/workflows/python-package-conda.yml
@@ -76,7 +76,7 @@ jobs:
         brew install hdf5
         python -m pip install --upgrade pip
         pip install -r test_requirements.txt -U --disable-pip-version-check
-        HDF5_DIR=/opt/homebrew/Cellar/hdf5/1.14.3 pip install -r requirements.txt -U --disable-pip-version-check
+        HDF5_DIR=/opt/homebrew/Cellar/hdf5/1.14.3_1 pip install -r requirements.txt -U --disable-pip-version-check
         pip install -e . --disable-pip-version-check
     - name: Test with pytest
       run: |

From 5c16d7a49ad50c8dbe010d87dbfd2c94c45874ba Mon Sep 17 00:00:00 2001
From: gouwens <nathang@alleninstitute.org>
Date: Mon, 29 Apr 2024 10:09:03 -0700
Subject: [PATCH 21/24] Update python-package-conda.yml

Trying to automatically get the hdf5 directory used by homebrew
---
 .github/workflows/python-package-conda.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
index c2b792fa..174affde 100644
--- a/.github/workflows/python-package-conda.yml
+++ b/.github/workflows/python-package-conda.yml
@@ -74,9 +74,10 @@ jobs:
       run: |
         conda install tqdm openjpeg ruamel.yaml
         brew install hdf5
+        export HDF5_DIR="$(brew --prefix hdf5)"
         python -m pip install --upgrade pip
         pip install -r test_requirements.txt -U --disable-pip-version-check
-        HDF5_DIR=/opt/homebrew/Cellar/hdf5/1.14.3_1 pip install -r requirements.txt -U --disable-pip-version-check
+        pip install -r requirements.txt -U --disable-pip-version-check
         pip install -e . --disable-pip-version-check
     - name: Test with pytest
       run: |

From 3b42675749d7db74d781925c4c929958c32864ef Mon Sep 17 00:00:00 2001
From: gouwens <nathang@alleninstitute.org>
Date: Mon, 29 Apr 2024 10:48:56 -0700
Subject: [PATCH 22/24] Update README.md

Modifying status badges
---
 README.md | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 5a7a2a52..30d178c0 100755
--- a/README.md
+++ b/README.md
@@ -1,5 +1,4 @@
-[![Documentation Status](https://readthedocs.org/projects/neuron-morphology/badge/?version=latest)](https://neuron-morphology.readthedocs.io/en/latest/?badge=latest) [![Allen Institute](https://circleci.com/gh/AllenInstitute/neuron_morphology.svg?style=svg)](https://app.circleci.com/pipelines/github/AllenInstitute/neuron_morphology) [![Build status](https://ci.appveyor.com/api/projects/status/7fekclwnq58p61ax?svg=true)](https://ci.appveyor.com/project/fcollman/neuron-morphology)
-
+[![Documentation Status](https://readthedocs.org/projects/neuron-morphology/badge/?version=latest)](https://neuron-morphology.readthedocs.io/en/latest/?badge=latest) ![build workflow](https://github.com/github/docs/actions/workflows/python-package-conda.yml/badge.svg)
 
 neuron_morphology
 =================

From 5ac3af2d1438c8b83f091ffa5e6ee612739f9f39 Mon Sep 17 00:00:00 2001
From: gouwens <nathang@alleninstitute.org>
Date: Mon, 29 Apr 2024 10:49:41 -0700
Subject: [PATCH 23/24] Update README.md

Forgot exclamation point
---
 README.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 30d178c0..ed7f963b 100755
--- a/README.md
+++ b/README.md
@@ -1,4 +1,5 @@
-[![Documentation Status](https://readthedocs.org/projects/neuron-morphology/badge/?version=latest)](https://neuron-morphology.readthedocs.io/en/latest/?badge=latest) ![build workflow](https://github.com/github/docs/actions/workflows/python-package-conda.yml/badge.svg)
+[![Documentation Status](https://readthedocs.org/projects/neuron-morphology/badge/?version=latest)](https://neuron-morphology.readthedocs.io/en/latest/?badge=latest)
+![build workflow](https://github.com/github/docs/actions/workflows/python-package-conda.yml/badge.svg)
 
 neuron_morphology
 =================

From e4f15fe278dd4e36334bf29b44c5974afbaee05c Mon Sep 17 00:00:00 2001
From: gouwens <nathang@alleninstitute.org>
Date: Mon, 29 Apr 2024 10:50:41 -0700
Subject: [PATCH 24/24] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index ed7f963b..f0eb47b2 100755
--- a/README.md
+++ b/README.md
@@ -1,5 +1,5 @@
 [![Documentation Status](https://readthedocs.org/projects/neuron-morphology/badge/?version=latest)](https://neuron-morphology.readthedocs.io/en/latest/?badge=latest)
-![build workflow](https://github.com/github/docs/actions/workflows/python-package-conda.yml/badge.svg)
+![build workflow](https://github.com/alleninstitute/neuron_morphology/actions/workflows/python-package-conda.yml/badge.svg)
 
 neuron_morphology
 =================