Merge pull request #1 from amathislab/v1.0rc

update v1.0rc

Author: AlexEMG

.github/ISSUE_TEMPLATE/bug_report.md

@@ -26,13 +26,7 @@ If applicable, add screenshots to help explain your problem.
 **Desktop (please complete the following information):**
  - OS: [e.g. iOS]
  - Browser [e.g. chrome, safari]
- - Version [e.g. 22]
-
-**Smartphone (please complete the following information):**
- - Device: [e.g. iPhone6]
- - OS: [e.g. iOS8.1]
- - Browser [e.g. stock browser, safari]
- - Version [e.g. 22]
+ - Version of DLC2action [e.g. 22]
 
 **Additional context**
 Add any other context about the problem here.

.github/ISSUE_TEMPLATE/custom.md

@@ -6,5 +6,3 @@ labels: ''
 assignees: ''
 
 ---
-
-

.github/ISSUE_TEMPLATE/feature_request.md

@@ -8,7 +8,7 @@ assignees: ''
 ---
 
 **Is your feature request related to a problem? Please describe.**
-A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+A clear and concise description of what the problem is. Ex. I'd really love if you I could [...]
 
 **Describe the solution you'd like**
 A clear and concise description of what you want to happen.

.github/workflows/create-docs.yml

@@ -3,18 +3,18 @@ name: create-docs
 on:
   push:
     branches:
-    - master
+    - main
 
 jobs:
   deploy-book:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
 
-    - name: Set up Python 3.9
+    - name: Set up Python 3.12
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
+        python-version: 3.12
 
     - name: Install dependencies
       run: |
@@ -27,7 +27,7 @@ jobs:
         pdoc --logo https://i.ibb.co/NstG5hz/03.png -o html_docs dlc2action
 
     - name: GitHub Pages action
-      uses: peaceiris/actions-gh-pages@v3.9.0
+      uses: peaceiris/actions-gh-pages@v3.12.0
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: ./html_docs

.github/workflows/test-package.yml

@@ -2,9 +2,9 @@ name: Test package
 
 on:
   push:
-    branches: [ master ]
+    branches: [ main ]
   pull_request:
-    branches: [ master ]
+    branches: [ main ]
 
 jobs:
   build:
@@ -14,7 +14,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-11, windows-latest]
-        python-version: [3.8, 3.9] 
+        python-version: [3.13] 
         include:
           - os: ubuntu-latest
             path: ~/.cache/pip
@@ -44,3 +44,4 @@ jobs:
         run: |
           pip install pytest
           python -m pytest
+          

.gitignore

@@ -1,16 +1,17 @@
 # custom
 /datasets
+/examples/OFT
+/examples/DLC2Action
+/fly_analysis-2021-07-15
 .vscode
 .DS_Store
 *.pkl
 *.pkl.json
 *.log.json
 work_dirs/
-experiments
-
+test.ipynb
 # Byte-compiled / optimized / DLL files for python
 __pycache__/
-*/__pycache__/
 *.py[cod]
 *$py.class
 
@@ -55,9 +56,9 @@ coverage.xml
 
 #PyCharm
 .idea
-
+._idea/*
+.circleci/*
 #Projects
-./projects/*
-examples/*/
-examples/*zip
-
+projects/*
+experiments
+test.ipynb

CONTRIBUTING.md

@@ -0,0 +1,29 @@
+# How to Contribute to DLC2Action
+
+DLC2Action is an actively developed package and we welcome community development and involvement.
+
+We are happy to receive code extensions, bug fixes, documentation updates, etc.
+
+## Setting up a development installation
+In order to make changes to `DLC2Action`, you will need to [fork](https://guides.github.com/activities/forking/#fork) the
+[repository](https://github.com/amathislab/dlc2action).
+
+If you are not familiar with `git`, we recommend reading up on [this guide](https://guides.github.com/introduction/git-handbook/#basic-git).
+
+Here are guidelines for installing DLC2Action locally on your own computer, where you can make changes to the code!
+
+> Note, before committing to DLC2Action, please be sure your code is formatted according to `black`. To learn more, see [`black`'s documentation](https://black.readthedocs.io/en/stable/).
+
+Now, please make a [pull request](https://github.com/amathislab/DLC2Action/pull/new/) that includes both a **summary of and changes to**:
+
+- How you modified the code and what new functionality it has.
+- DOCSTRING update for your change
+- A working example of how it works for users.
+- If it's a function that also can be used in downstream steps (i.e. could be plotted) we ask you (1) highlight this, and (2) ideally you provide that functionality as well.
+
+**Review & Formatting:**
+
+- Please run black on the code to conform to our Black code style (see more at https://pypi.org/project/black/).
+- Please assign a reviewer, typically @andybonnetto or @AlexEMG!
+
+Thanks for your contributions! 

Dockerfile

@@ -0,0 +1,14 @@
+FROM nvcr.io/nvidia/pytorch:24.11-py3
+
+RUN mkdir -p /DLC2action
+COPY . /DLC2action
+WORKDIR /DLC2action
+
+# Install required packages
+RUN apt update
+RUN apt install python3-pip -y
+RUN pip install -e .
+
+RUN apt-get install ffmpeg libsm6 libxext6  -y
+RUN apt-get install -y git
+RUN apt-get install vim -y

LICENSE.yml

@@ -1,4 +1,4 @@
-Copyright 2020-present by A. Mathis Group and contributors. All rights reserved.
+Copyright 2025-present by A. Mathis Group and contributors. All rights reserved.
 
 This project and all its files are licensed under GNU AGPLv3 or later version. A copy is included in dlc2action/LICENSE.AGPL.
 

MANIFEST.in

@@ -1 +1 @@
-recursive-include dlc2action/config *.yaml
+recursive-include dlc2action/config *.yaml