From 7adbec494ac0fbb467980dce8d0f5405ceb5ddbc Mon Sep 17 00:00:00 2001
From: YektaY <yektay1@gmail.com>
Date: Mon, 25 Sep 2023 11:34:25 -0700
Subject: [PATCH 01/18] starting to set up the pre-commit and running tests in
 github actions

---
 .github/workflows/pre-commit.yml | 14 ++++++++
 .github/workflows/run-test.yml   | 60 ++++++++++++++++++++++++++++++++
 .pre-commit-config.yaml          | 18 ++++++++++
 run_tests.py                     | 21 +++++++++++
 windows-dev-requirements.txt     |  5 +++
 5 files changed, 118 insertions(+)
 create mode 100644 .github/workflows/pre-commit.yml
 create mode 100644 .github/workflows/run-test.yml
 create mode 100644 .pre-commit-config.yaml
 create mode 100644 run_tests.py
 create mode 100644 windows-dev-requirements.txt

diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
new file mode 100644
index 00000000..04f86a39
--- /dev/null
+++ b/.github/workflows/pre-commit.yml
@@ -0,0 +1,14 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v3
+    - uses: pre-commit/action@v3.0.0
\ No newline at end of file
diff --git a/.github/workflows/run-test.yml b/.github/workflows/run-test.yml
new file mode 100644
index 00000000..66f24d75
--- /dev/null
+++ b/.github/workflows/run-test.yml
@@ -0,0 +1,60 @@
+# This workflow will install pydm dependencies, lint with flake8, and run the test suite, for all combinations
+# of operating systems and version numbers specified in the matrix
+
+name: Build Status
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    if: ${{ github.repository == 'slaclab/Badger' }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: [3.9]
+        pyqt-version: [5.12.3, 5.15.7]
+    env:
+      DISPLAY: ':99.0'
+      QT_MAC_WANTS_LAYER: 1  # PyQT gui tests involving qtbot interaction on macOS will fail without this
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Setup conda
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+        miniforge-variant: Mambaforge
+        miniforge-version: latest
+        activate-environment: badger-env
+    - name: Install python packages
+      shell: bash -el {0}
+      run: |
+        if [ "$RUNNER_OS" == "Windows" ]; then
+          mamba install flake8 zipp pyqt=${{ matrix.pyqt-version }}
+          mamba install --file requirements.txt --file windows-dev-requirements.txt
+        else
+          mamba install flake8 zipp pyqt=${{ matrix.pyqt-version }} $(cat requirements.txt dev-requirements.txt)
+        fi
+    - name: Install packages for testing a pyqt app on linux
+      shell: bash -el {0}
+      run: |
+        if [ "$RUNNER_OS" == "Linux" ]; then
+          sudo apt install xvfb herbstluftwm libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xfixes0 x11-utils
+          sudo /sbin/start-stop-daemon --start --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1024x768x24 -ac +extension GLX +render -noreset
+          sleep 3
+          sudo /sbin/start-stop-daemon --start --pidfile /tmp/custom_herbstluftwm_99.pid --make-pidfile --background --exec /usr/bin/herbstluftwm
+          sleep 1
+        fi
+    - name: Test with pytest
+      shell: bash -el {0}
+      run: |
+        python run_tests.py
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 00000000..6ce4ae55
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,18 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+    -   id: end-of-file-fixer
+        files: '\.(py|txt)$' # Only run on .py and .txt files	
+    -   id: trailing-whitespace
+        files: '\.(py|txt)$' # Only run on .py and .txt files
+-   repo: https://github.com/psf/black
+    rev: 23.7.0
+    hooks:
+    -   id: black
+        args: [--line-length, '120']
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.287
+    hooks:
+    -   id: ruff
+        args: [--line-length, '120', --fix, --exit-non-zero-on-fix]
\ No newline at end of file
diff --git a/run_tests.py b/run_tests.py
new file mode 100644
index 00000000..dd7494f4
--- /dev/null
+++ b/run_tests.py
@@ -0,0 +1,21 @@
+#!/usr/bin/env python
+import sys
+import pytest
+
+if __name__ == "__main__":
+    # Show output results from every test function
+    # Show the message output for skipped and expected failures
+    args = ["-v", "-vrxs"]
+
+    # Add extra arguments
+    if len(sys.argv) > 1:
+        args.extend(sys.argv[1:])
+
+    # Show coverage
+    if "--show-cov" in args:
+        args.extend(["--cov=archive_viewer", "--cov-report", "term-missing"])
+        args.remove("--show-cov")
+
+    print("pytest arguments: {}".format(args))
+
+    sys.exit(pytest.main(args))
diff --git a/windows-dev-requirements.txt b/windows-dev-requirements.txt
new file mode 100644
index 00000000..456c813e
--- /dev/null
+++ b/windows-dev-requirements.txt
@@ -0,0 +1,5 @@
+codecov
+pytest>=3.6
+pytest-qt
+pytest-cov
+pytest-timeout

From 090dfe934cfeccf0186dda173f5a1b5a347e3502 Mon Sep 17 00:00:00 2001
From: YektaY <yektay1@gmail.com>
Date: Mon, 25 Sep 2023 11:56:51 -0700
Subject: [PATCH 02/18] added a requirements.txt

---
 requirements.txt | 12 ++++++++++++
 1 file changed, 12 insertions(+)
 create mode 100644 requirements.txt

diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 00000000..31de29b9
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,12 @@
+pandas
+pyyaml
+coolname
+pyqt5
+pyqtgraph
+qdarkstyle
+pillow
+requests
+tqdm
+xopt
+pytest
+pytest-qt
\ No newline at end of file

From cc5985dc3ff4c1fdbab8861074e07324b24db813 Mon Sep 17 00:00:00 2001
From: YektaY <yektay1@gmail.com>
Date: Mon, 25 Sep 2023 13:34:58 -0700
Subject: [PATCH 03/18] set vertion of pyqt to test with to 5.15.9

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

diff --git a/.github/workflows/run-test.yml b/.github/workflows/run-test.yml
index 66f24d75..19281773 100644
--- a/.github/workflows/run-test.yml
+++ b/.github/workflows/run-test.yml
@@ -21,7 +21,7 @@ jobs:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
         python-version: [3.9]
-        pyqt-version: [5.12.3, 5.15.7]
+        pyqt-version: [5.15.9]
     env:
       DISPLAY: ':99.0'
       QT_MAC_WANTS_LAYER: 1  # PyQT gui tests involving qtbot interaction on macOS will fail without this

From 6fe925da71ca97773a3ead6cb4d32547e5b33103 Mon Sep 17 00:00:00 2001
From: YektaY <yektay1@gmail.com>
Date: Mon, 25 Sep 2023 13:41:47 -0700
Subject: [PATCH 04/18] changed comment and branch name

---
 .github/workflows/run-test.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/run-test.yml b/.github/workflows/run-test.yml
index 19281773..31fa9cb2 100644
--- a/.github/workflows/run-test.yml
+++ b/.github/workflows/run-test.yml
@@ -5,9 +5,9 @@ name: Build Status
 
 on:
   push:
-    branches: [ "main" ]
+    branches: [ "master" ]
   pull_request:
-    branches: [ "main" ]
+    branches: [ "master" ]
 
 permissions:
   contents: read

From d63bb12024806a7e46e84eca1617db319d201bca Mon Sep 17 00:00:00 2001
From: YektaY <yektay1@gmail.com>
Date: Mon, 25 Sep 2023 13:45:03 -0700
Subject: [PATCH 05/18] small change

---
 run_tests.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/run_tests.py b/run_tests.py
index dd7494f4..858f467c 100644
--- a/run_tests.py
+++ b/run_tests.py
@@ -13,7 +13,7 @@
 
     # Show coverage
     if "--show-cov" in args:
-        args.extend(["--cov=archive_viewer", "--cov-report", "term-missing"])
+        args.extend(["--cov=badger", "--cov-report", "term-missing"])
         args.remove("--show-cov")
 
     print("pytest arguments: {}".format(args))

From 6a449662821fd780bfe66293a6adbb95c1d017f3 Mon Sep 17 00:00:00 2001
From: YektaY <yektay1@gmail.com>
Date: Mon, 25 Sep 2023 13:48:54 -0700
Subject: [PATCH 06/18] change branch name

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

diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
index 04f86a39..ae761691 100644
--- a/.github/workflows/pre-commit.yml
+++ b/.github/workflows/pre-commit.yml
@@ -3,7 +3,7 @@ name: pre-commit
 on:
   pull_request:
   push:
-    branches: [main]
+    branches: [master]
 
 jobs:
   pre-commit:

From 37e9242deb4504b80e7d2d3ee5119da24693c990 Mon Sep 17 00:00:00 2001
From: YektaY <yektay1@gmail.com>
Date: Mon, 25 Sep 2023 13:49:39 -0700
Subject: [PATCH 07/18] small changes

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

diff --git a/.github/workflows/run-test.yml b/.github/workflows/run-test.yml
index 31fa9cb2..0894e56c 100644
--- a/.github/workflows/run-test.yml
+++ b/.github/workflows/run-test.yml
@@ -1,4 +1,4 @@
-# This workflow will install pydm dependencies, lint with flake8, and run the test suite, for all combinations
+# This workflow will install badger dependencies, lint with flake8, and run the test suite, for all combinations
 # of operating systems and version numbers specified in the matrix
 
 name: Build Status

From 6ded482271c54456882e01330a80d1af202e8b24 Mon Sep 17 00:00:00 2001
From: YektaY <yektay1@gmail.com>
Date: Tue, 26 Sep 2023 16:59:00 -0700
Subject: [PATCH 08/18] started to set up the a site for badger documentation
 using mkdocs

---
 .github/workflows/gh-pages.yml | 35 ++++++++++++++++++++++++++++
 .github/workflows/run-test.yml |  2 +-
 doc-environment.yml            |  7 ++++++
 docs/core.md                   |  3 +++
 docs/index.md                  |  1 +
 mkdocs.yml                     | 42 ++++++++++++++++++++++++++++++++++
 6 files changed, 89 insertions(+), 1 deletion(-)
 create mode 100644 .github/workflows/gh-pages.yml
 create mode 100644 doc-environment.yml
 create mode 100644 docs/core.md
 create mode 100644 docs/index.md
 create mode 100644 mkdocs.yml

diff --git a/.github/workflows/gh-pages.yml b/.github/workflows/gh-pages.yml
new file mode 100644
index 00000000..87c65b8a
--- /dev/null
+++ b/.github/workflows/gh-pages.yml
@@ -0,0 +1,35 @@
+name: Publish Documentation
+
+on:
+  push:
+    branches:
+      - master
+
+jobs:
+  deploy:
+    if: ${{ github.repository == 'slaclab/Badger' }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [3.9]
+    steps:
+      - uses: actions/checkout@v3
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+          miniforge-variant: Mambaforge
+          channels: conda-forge
+          activate-environment: badger-doc
+          environment-file: doc-environment.yml
+
+      - name: Build Docs
+        shell: bash -l {0}
+        run: |
+          mkdocs build
+
+      - name: Deploy to gh-pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./site/
\ No newline at end of file
diff --git a/.github/workflows/run-test.yml b/.github/workflows/run-test.yml
index 0894e56c..ecbf0038 100644
--- a/.github/workflows/run-test.yml
+++ b/.github/workflows/run-test.yml
@@ -20,7 +20,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: [3.9]
+        python-version: [3.9, 3.11]
         pyqt-version: [5.15.9]
     env:
       DISPLAY: ':99.0'
diff --git a/doc-environment.yml b/doc-environment.yml
new file mode 100644
index 00000000..1a191a0f
--- /dev/null
+++ b/doc-environment.yml
@@ -0,0 +1,7 @@
+name: badger-dev
+  - mkdocs
+  - mkdocs-material
+  - mkdocstrings
+  - mkdocstrings-python
+
+    
\ No newline at end of file
diff --git a/docs/core.md b/docs/core.md
new file mode 100644
index 00000000..3233229f
--- /dev/null
+++ b/docs/core.md
@@ -0,0 +1,3 @@
+# Core
+
+::: src.badgre.core
\ No newline at end of file
diff --git a/docs/index.md b/docs/index.md
new file mode 100644
index 00000000..f77d89aa
--- /dev/null
+++ b/docs/index.md
@@ -0,0 +1 @@
+[Badger](https://github.com/slaclab/Badger) is an application 
\ No newline at end of file
diff --git a/mkdocs.yml b/mkdocs.yml
new file mode 100644
index 00000000..5da71d95
--- /dev/null
+++ b/mkdocs.yml
@@ -0,0 +1,42 @@
+site_name: Badger
+repo_url: https://github.com/slaclab/Badger
+repo_name: slaclab/Badger
+
+nav:
+    - Home: index.md
+    - Installation: installation.md
+    - API Reference:
+        - Core: core.md
+
+theme:
+  icon:
+    repo: fontawesome/brands/github
+  name: material
+
+  features:
+    - navigation.top
+    - navigation.tabs
+    - navigation.indexes
+  palette:
+    - media: "(prefers-color-scheme: light)"
+      scheme: default
+      primary: black
+      toggle:
+        icon: material/toggle-switch-off-outline
+        name: Switch to dark mode
+    - media: "(prefers-color-scheme: dark)"
+      scheme: slate
+      primary: black
+      toggle:
+        icon: material/toggle-switch
+        name: Switch to light mode
+
+markdown_extensions:
+  - pymdownx.highlight
+  - pymdownx.superfences
+
+plugins:
+    - search
+    - mkdocstrings:
+        default_handler: python
+

From c7dd80f10db618318f616c9cceabc47c85d1c4af Mon Sep 17 00:00:00 2001
From: YektaY <yektay1@gmail.com>
Date: Thu, 28 Sep 2023 15:10:30 -0700
Subject: [PATCH 09/18] removed changes to docs for now, will reimplement in
 another PR useing Badgers existing docs site

---
 .github/workflows/gh-pages.yml | 35 ----------------------------
 doc-environment.yml            |  7 ------
 docs/core.md                   |  3 ---
 docs/index.md                  |  1 -
 mkdocs.yml                     | 42 ----------------------------------
 5 files changed, 88 deletions(-)
 delete mode 100644 .github/workflows/gh-pages.yml
 delete mode 100644 doc-environment.yml
 delete mode 100644 docs/core.md
 delete mode 100644 docs/index.md
 delete mode 100644 mkdocs.yml

diff --git a/.github/workflows/gh-pages.yml b/.github/workflows/gh-pages.yml
deleted file mode 100644
index 87c65b8a..00000000
--- a/.github/workflows/gh-pages.yml
+++ /dev/null
@@ -1,35 +0,0 @@
-name: Publish Documentation
-
-on:
-  push:
-    branches:
-      - master
-
-jobs:
-  deploy:
-    if: ${{ github.repository == 'slaclab/Badger' }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [ubuntu-latest]
-        python-version: [3.9]
-    steps:
-      - uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          python-version: ${{ matrix.python-version }}
-          miniforge-variant: Mambaforge
-          channels: conda-forge
-          activate-environment: badger-doc
-          environment-file: doc-environment.yml
-
-      - name: Build Docs
-        shell: bash -l {0}
-        run: |
-          mkdocs build
-
-      - name: Deploy to gh-pages
-        uses: peaceiris/actions-gh-pages@v3
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ./site/
\ No newline at end of file
diff --git a/doc-environment.yml b/doc-environment.yml
deleted file mode 100644
index 1a191a0f..00000000
--- a/doc-environment.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-name: badger-dev
-  - mkdocs
-  - mkdocs-material
-  - mkdocstrings
-  - mkdocstrings-python
-
-    
\ No newline at end of file
diff --git a/docs/core.md b/docs/core.md
deleted file mode 100644
index 3233229f..00000000
--- a/docs/core.md
+++ /dev/null
@@ -1,3 +0,0 @@
-# Core
-
-::: src.badgre.core
\ No newline at end of file
diff --git a/docs/index.md b/docs/index.md
deleted file mode 100644
index f77d89aa..00000000
--- a/docs/index.md
+++ /dev/null
@@ -1 +0,0 @@
-[Badger](https://github.com/slaclab/Badger) is an application 
\ No newline at end of file
diff --git a/mkdocs.yml b/mkdocs.yml
deleted file mode 100644
index 5da71d95..00000000
--- a/mkdocs.yml
+++ /dev/null
@@ -1,42 +0,0 @@
-site_name: Badger
-repo_url: https://github.com/slaclab/Badger
-repo_name: slaclab/Badger
-
-nav:
-    - Home: index.md
-    - Installation: installation.md
-    - API Reference:
-        - Core: core.md
-
-theme:
-  icon:
-    repo: fontawesome/brands/github
-  name: material
-
-  features:
-    - navigation.top
-    - navigation.tabs
-    - navigation.indexes
-  palette:
-    - media: "(prefers-color-scheme: light)"
-      scheme: default
-      primary: black
-      toggle:
-        icon: material/toggle-switch-off-outline
-        name: Switch to dark mode
-    - media: "(prefers-color-scheme: dark)"
-      scheme: slate
-      primary: black
-      toggle:
-        icon: material/toggle-switch
-        name: Switch to light mode
-
-markdown_extensions:
-  - pymdownx.highlight
-  - pymdownx.superfences
-
-plugins:
-    - search
-    - mkdocstrings:
-        default_handler: python
-

From b5251581a93e68dac67cebf905c21b10bc122579 Mon Sep 17 00:00:00 2001
From: YektaY <yektay1@gmail.com>
Date: Tue, 24 Oct 2023 14:19:31 -0700
Subject: [PATCH 10/18] switched to running tests for push and pr for all
 branches instead of just master

---
 .github/workflows/run-test.yml | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/run-test.yml b/.github/workflows/run-test.yml
index ecbf0038..b213a9af 100644
--- a/.github/workflows/run-test.yml
+++ b/.github/workflows/run-test.yml
@@ -5,9 +5,9 @@ name: Build Status
 
 on:
   push:
-    branches: [ "master" ]
+    branches: [ "**" ]
   pull_request:
-    branches: [ "master" ]
+    branches: [ "**" ]
 
 permissions:
   contents: read
@@ -21,7 +21,6 @@ jobs:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
         python-version: [3.9, 3.11]
-        pyqt-version: [5.15.9]
     env:
       DISPLAY: ':99.0'
       QT_MAC_WANTS_LAYER: 1  # PyQT gui tests involving qtbot interaction on macOS will fail without this
@@ -39,10 +38,10 @@ jobs:
       shell: bash -el {0}
       run: |
         if [ "$RUNNER_OS" == "Windows" ]; then
-          mamba install flake8 zipp pyqt=${{ matrix.pyqt-version }}
+          mamba install flake8 zipp 
           mamba install --file requirements.txt --file windows-dev-requirements.txt
         else
-          mamba install flake8 zipp pyqt=${{ matrix.pyqt-version }} $(cat requirements.txt dev-requirements.txt)
+          mamba install flake8 zipp $(cat requirements.txt dev-requirements.txt)
         fi
     - name: Install packages for testing a pyqt app on linux
       shell: bash -el {0}

From 8122fbcb3e5690ef052e37a0457a0343c5a2ad03 Mon Sep 17 00:00:00 2001
From: YektaY <yektay1@gmail.com>
Date: Wed, 25 Oct 2023 15:44:58 -0700
Subject: [PATCH 11/18] fixed issue with installing pyqt5 in the text
 environment

---
 .github/workflows/run-test.yml | 4 ++++
 requirements.txt               | 1 -
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/run-test.yml b/.github/workflows/run-test.yml
index b213a9af..32264696 100644
--- a/.github/workflows/run-test.yml
+++ b/.github/workflows/run-test.yml
@@ -43,6 +43,10 @@ jobs:
         else
           mamba install flake8 zipp $(cat requirements.txt dev-requirements.txt)
         fi
+    - name: Install pyqt5
+      shell: bash -el {0}
+      run: |
+          pip install PyQt5
     - name: Install packages for testing a pyqt app on linux
       shell: bash -el {0}
       run: |
diff --git a/requirements.txt b/requirements.txt
index 31de29b9..60ef9806 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,7 +1,6 @@
 pandas
 pyyaml
 coolname
-pyqt5
 pyqtgraph
 qdarkstyle
 pillow

From 70ed6fad0b13f341e9d4d85f3ba0f4bf8e06bf5d Mon Sep 17 00:00:00 2001
From: YektaY <yektay1@gmail.com>
Date: Thu, 26 Oct 2023 14:07:16 -0700
Subject: [PATCH 12/18] fixed issue with windows test environment

---
  environment-dev.yml           | 5 +++++
 .github/workflows/run-test.yml | 1 +
 windows-dev-requirements.txt   | 1 +
 3 files changed, 7 insertions(+)
 create mode 100644  environment-dev.yml

diff --git a/ environment-dev.yml b/ environment-dev.yml
new file mode 100644
index 00000000..a3f17cc8
--- /dev/null
+++ b/ environment-dev.yml	
@@ -0,0 +1,5 @@
+name: badger-env
+channels:
+  - conda-forge
+  - defaults
+  - pytorch
diff --git a/.github/workflows/run-test.yml b/.github/workflows/run-test.yml
index 32264696..e9ef4e20 100644
--- a/.github/workflows/run-test.yml
+++ b/.github/workflows/run-test.yml
@@ -34,6 +34,7 @@ jobs:
         miniforge-variant: Mambaforge
         miniforge-version: latest
         activate-environment: badger-env
+        environment-file: environment-dev.yml
     - name: Install python packages
       shell: bash -el {0}
       run: |
diff --git a/windows-dev-requirements.txt b/windows-dev-requirements.txt
index 456c813e..e9fd20a1 100644
--- a/windows-dev-requirements.txt
+++ b/windows-dev-requirements.txt
@@ -1,3 +1,4 @@
+pytorch
 codecov
 pytest>=3.6
 pytest-qt

From bbcc50f3174e372af6aacc1ce51c41a155153641 Mon Sep 17 00:00:00 2001
From: YektaY <yektay1@gmail.com>
Date: Thu, 26 Oct 2023 14:09:54 -0700
Subject: [PATCH 13/18] enforce xopt 2.0 or later to address windows test issue

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 60ef9806..d1b0e161 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -6,6 +6,6 @@ qdarkstyle
 pillow
 requests
 tqdm
-xopt
+xopt>=2.0.0
 pytest
 pytest-qt
\ No newline at end of file

From 0a88e16b5005245cd58dbddd8f3154f65898f726 Mon Sep 17 00:00:00 2001
From: YektaY <yektay1@gmail.com>
Date: Fri, 27 Oct 2023 11:31:16 -0700
Subject: [PATCH 14/18] changed file name, current name seemed to have caused
 an issue

---
  environment-dev.yml =>  environment.yml | 0
 .github/workflows/run-test.yml           | 2 +-
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename  environment-dev.yml =>  environment.yml (100%)

diff --git a/ environment-dev.yml b/ environment.yml
similarity index 100%
rename from  environment-dev.yml
rename to  environment.yml
diff --git a/.github/workflows/run-test.yml b/.github/workflows/run-test.yml
index e9ef4e20..7f8d5fdb 100644
--- a/.github/workflows/run-test.yml
+++ b/.github/workflows/run-test.yml
@@ -34,7 +34,7 @@ jobs:
         miniforge-variant: Mambaforge
         miniforge-version: latest
         activate-environment: badger-env
-        environment-file: environment-dev.yml
+        environment-file: environment.yml
     - name: Install python packages
       shell: bash -el {0}
       run: |

From 8060041a1e9b8e030cbad199a2837b911729bb32 Mon Sep 17 00:00:00 2001
From: YektaY <yektay1@gmail.com>
Date: Fri, 27 Oct 2023 11:38:23 -0700
Subject: [PATCH 15/18] there was a blank space in front of the file name...

---
  environment.yml | 5 -----
 1 file changed, 5 deletions(-)
 delete mode 100644  environment.yml

diff --git a/ environment.yml b/ environment.yml
deleted file mode 100644
index a3f17cc8..00000000
--- a/ environment.yml	
+++ /dev/null
@@ -1,5 +0,0 @@
-name: badger-env
-channels:
-  - conda-forge
-  - defaults
-  - pytorch

From d3b8ad4b294f764bfb1192a0c7b3f1a9be4b12d1 Mon Sep 17 00:00:00 2001
From: YektaY <yektay1@gmail.com>
Date: Fri, 27 Oct 2023 11:41:03 -0700
Subject: [PATCH 16/18] file was not added in the last commit

---
 environment.yml | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 environment.yml

diff --git a/environment.yml b/environment.yml
new file mode 100644
index 00000000..a3f17cc8
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,5 @@
+name: badger-env
+channels:
+  - conda-forge
+  - defaults
+  - pytorch

From a722071ebbff8adccb7feb9450d828a01baa207d Mon Sep 17 00:00:00 2001
From: YektaY <yektay1@gmail.com>
Date: Tue, 5 Dec 2023 10:19:49 -0800
Subject: [PATCH 17/18] changed environment file name

---
 .github/workflows/run-test.yml | 2 +-
 environment.yml                | 5 -----
 2 files changed, 1 insertion(+), 6 deletions(-)
 delete mode 100644 environment.yml

diff --git a/.github/workflows/run-test.yml b/.github/workflows/run-test.yml
index 7f8d5fdb..e9ef4e20 100644
--- a/.github/workflows/run-test.yml
+++ b/.github/workflows/run-test.yml
@@ -34,7 +34,7 @@ jobs:
         miniforge-variant: Mambaforge
         miniforge-version: latest
         activate-environment: badger-env
-        environment-file: environment.yml
+        environment-file: environment-dev.yml
     - name: Install python packages
       shell: bash -el {0}
       run: |
diff --git a/environment.yml b/environment.yml
deleted file mode 100644
index a3f17cc8..00000000
--- a/environment.yml
+++ /dev/null
@@ -1,5 +0,0 @@
-name: badger-env
-channels:
-  - conda-forge
-  - defaults
-  - pytorch

From 2db92b6e3ba5fbf6e19d775e6277ac12b55739c7 Mon Sep 17 00:00:00 2001
From: YektaY <yektay1@gmail.com>
Date: Tue, 5 Dec 2023 10:26:23 -0800
Subject: [PATCH 18/18] added missing environment-dev.yml file

---
 environment-dev.yml | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 environment-dev.yml

diff --git a/environment-dev.yml b/environment-dev.yml
new file mode 100644
index 00000000..a3f17cc8
--- /dev/null
+++ b/environment-dev.yml
@@ -0,0 +1,5 @@
+name: badger-env
+channels:
+  - conda-forge
+  - defaults
+  - pytorch