Align develop and main

.conda/README.md

@@ -3,7 +3,7 @@ This folder defines the conda package build for Linux and Windows. There are run
 To build, first go to the base repo directory and install the build environment:
 
 ```
-mamba env create -f environment_build.yml -n sleap_build && conda activate sleap_build
+conda env create -f environment_build.yml -n sleap_build && conda activate sleap_build
 ```
 
 And finally, run the build command pointing to this directory:
@@ -15,7 +15,7 @@ conda build .conda --output-folder build -c conda-forge -c nvidia -c https://con
 To install the local package:
 
 ```
-mamba create -n sleap_0 -c conda-forge -c nvidia -c ./build -c https://conda.anaconda.org/sleap/ -c anaconda sleap=x.x.x
+conda create -n sleap_0 -c conda-forge -c nvidia -c ./build -c https://conda.anaconda.org/sleap/ -c anaconda sleap=x.x.x
 ```
 
 replacing x.x.x with the version of SLEAP that you just built.

.conda/condarc.yaml

@@ -1,5 +1,6 @@
 channels:
   - conda-forge
   - nvidia
+  - https://conda.anaconda.org/sleap/label/dev
   - sleap
   - anaconda

.conda/meta.yaml

@@ -16,7 +16,7 @@ source:
   path: ../
 
 build:
-  number: 1
+  number: 0
 
 requirements:
   host:
@@ -32,12 +32,12 @@ requirements:
     # unnecessary pypi packages are installed via the build script (bld.bat, build.sh)
     - conda-forge::attrs ==21.4.0
     - conda-forge::cattrs ==1.1.1
-    - conda-forge::h5py ==3.1  # [not win]
-    - conda-forge::imgaug ==0.4.0
+    - conda-forge::h5py ==3.7.0
+    - conda-forge::imageio-ffmpeg # Required for imageio to read/write videos with ffmpeg
     - conda-forge::jsmin
     - conda-forge::jsonpickle ==1.2
     - conda-forge::networkx
-    - conda-forge::opencv
+    - conda-forge::opencv <4.9.0
     - conda-forge::pandas
     - conda-forge::pillow >=8.3.2
     - conda-forge::psutil
@@ -53,20 +53,24 @@ requirements:
     - conda-forge::scikit-learn ==1.0
     - conda-forge::scikit-video
     - conda-forge::seaborn
+    - conda-forge::qudida
+    - conda-forge::albumentations
+    - conda-forge::ndx-pose <0.2.0
+    - conda-forge::importlib-metadata ==4.11.4
   run:
     - conda-forge::python ==3.7.12  # Run into _MAX_WINDOWS_WORKERS not found if <
     - conda-forge::attrs ==21.4.0
     - conda-forge::cattrs ==1.1.1
+    - conda-forge::imageio-ffmpeg # Required for imageio to read/write videos with ffmpeg
     - conda-forge::cudatoolkit ==11.3.1
     - conda-forge::cudnn=8.2.1
     - nvidia::cuda-nvcc=11.3
-    - conda-forge::h5py ==3.1  # [not win]
-    - conda-forge::imgaug ==0.4.0
+    - conda-forge::h5py ==3.7.0
     - conda-forge::jsmin
     - conda-forge::jsonpickle ==1.2
     - conda-forge::networkx
     - numpy >=1.19.5,<1.23.0  # Linux likes anaconda, windows likes conda-forge
-    - conda-forge::opencv
+    - conda-forge::opencv <4.9.0
     - conda-forge::pandas
     - conda-forge::pillow >=8.3.2
     - conda-forge::psutil
@@ -82,9 +86,15 @@ requirements:
     - conda-forge::scikit-learn ==1.0
     - conda-forge::scikit-video
     - conda-forge::seaborn
-    - sleap::tensorflow >=2.6.3,<2.11  # No windows GPU support for >2.10, sleap channel has 2.6.3
+    - sleap/label/dev::tensorflow ==2.7.0  # TODO: Switch to main label when updated
     - conda-forge::tensorflow-hub <0.14.0  # Causes pynwb conflicts on linux GH-1446
+    - conda-forge::qudida
+    - conda-forge::albumentations
+    - conda-forge::ndx-pose <0.2.0
+    - conda-forge::importlib-metadata ==4.11.4
 
-test:
-  imports:
-    - sleap
+# This no longer works so we have moved it to the build workflow
+# https://github.com/talmolab/sleap/pull/1744
+# test:
+#   imports:
+#     - sleap

.conda_mac/build.sh

@@ -2,7 +2,6 @@
 
 # Install anything that didn't get conda installed via pip.
 # We need to turn pip index back on because Anaconda turns it off for some reason. 
-
 export PIP_NO_INDEX=False
 export PIP_NO_DEPENDENCIES=False
 export PIP_IGNORE_INSTALLED=False

.conda_mac/condarc.yaml

@@ -1,4 +1,3 @@
-# This file is not used at the moment, but when github actions can be used to build the package, it needs to be listed.
 # https://github.com/github/roadmap/issues/528
 
 channels:

.conda_mac/meta.yaml

@@ -16,14 +16,14 @@ about:
   summary: {{ data.get('description') }}
 
 build:
-  number: 1
+  number: 0
 
 source:
   path: ../
 
 requirements:
   host:  
-    - conda-forge::python ~=3.9
+    - conda-forge::python >=3.9.0, <3.10.0
     - anaconda::numpy >=1.19.5,<1.23.0
     - conda-forge::setuptools
     - conda-forge::packaging
@@ -34,11 +34,11 @@ requirements:
     - conda-forge::attrs >=21.2.0
     - conda-forge::cattrs ==1.1.1
     - conda-forge::h5py
-    - conda-forge::imgaug ==0.4.0
+    - conda-forge::imageio-ffmpeg # Required for imageio to read/write videos with ffmpeg
     - conda-forge::jsmin
     - conda-forge::jsonpickle ==1.2
     - conda-forge::keras <2.10.0,>=2.9.0rc0  # Required by tensorflow-macos
-    - conda-forge::networkx
+    - conda-forge::networkx <3.3
     - conda-forge::opencv
     - conda-forge::pandas
     - conda-forge::pillow
@@ -55,17 +55,20 @@ requirements:
     - conda-forge::scikit-learn ==1.0
     - conda-forge::scikit-video
     - conda-forge::seaborn
+    - conda-forge::qudida
+    - conda-forge::albumentations
+    - conda-forge::ndx-pose <0.2.0
 
   run:
-    - conda-forge::python ~=3.9
+    - conda-forge::python >=3.9.0, <3.10.0
     - conda-forge::attrs >=21.2.0
     - conda-forge::cattrs ==1.1.1
     - conda-forge::h5py
-    - conda-forge::imgaug ==0.4.0
+    - conda-forge::imageio-ffmpeg # Required for imageio to read/write videos with ffmpeg
     - conda-forge::jsmin
     - conda-forge::jsonpickle ==1.2
     - conda-forge::keras <2.10.0,>=2.9.0rc0  # Required by tensorflow-macos
-    - conda-forge::networkx
+    - conda-forge::networkx <3.3
     - anaconda::numpy >=1.19.5,<1.23.0
     - conda-forge::opencv
     - conda-forge::pandas
@@ -83,8 +86,11 @@ requirements:
     - conda-forge::scikit-learn ==1.0
     - conda-forge::scikit-video
     - conda-forge::seaborn
-    - conda-forge::tensorflow-hub
+    # - conda-forge::tensorflow-hub  # pulls in tensorflow cpu from conda-forge
+    - conda-forge::qudida
+    - conda-forge::albumentations
+    - conda-forge::ndx-pose <0.2.0
 
-test:
-  imports:
-    - sleap
+# test:
+#   imports:
+#     - sleap

.github/ISSUE_TEMPLATE/bug_report.md

@@ -25,15 +25,15 @@ Tell us a little about the system you're using.
 Please include information about how you installed.
  -->
 
-- OS:
+-   OS:
 <!-- [e.g. ubuntu 20.04, macOS 11.0] -->
-- Version(s):
-<!-- e.g. [SLEAP v1.3.3, python 3.8] --->
-- SLEAP installation method (listed [here](https://sleap.ai/installation.html#)):
-  - [ ] [Conda from package](https://sleap.ai/installation.html#conda-package)
-  - [ ] [Conda from source](https://sleap.ai/installation.html#conda-from-source)
-  - [ ] [pip package](https://sleap.ai/installation.html#pip-package)
-  - [ ] [Apple Silicon Macs](https://sleap.ai/installation.html#apple-silicon-macs)
+-   Version(s):
+<!-- e.g. [SLEAP v1.4.1, python 3.8] --->
+-   SLEAP installation method (listed [here](https://sleap.ai/installation.html#)):
+    -   [ ] [Conda from package](https://sleap.ai/installation.html#conda-package)
+    -   [ ] [Conda from source](https://sleap.ai/installation.html#conda-from-source)
+    -   [ ] [pip package](https://sleap.ai/installation.html#pip-package)
+    -   [ ] [Apple Silicon Macs](https://sleap.ai/installation.html#apple-silicon-macs)
 
 <details><summary>Environment packages</summary>
 <!-- For reproduction, it's useful to have the full environment. For example, the output of `pip freeze` or `conda list` --->

.github/workflows/archive/comment-template.yml

@@ -0,0 +1,71 @@
+name: Reusable Comment Workflow
+
+on:
+  workflow_call:
+    inputs:
+      subject_id:
+        required: true
+        type: string
+      body_prefix:
+        required: true
+        type: string
+      comment_type:
+        required: true
+        type: string
+
+jobs:
+  comment:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Post a comment
+        uses: actions/github-script@v6
+        with:
+          script: |
+            const { owner, repo } = context.repo;
+            const subject_id = '${{ inputs.subject_id }}';
+            const comment_type = '${{ inputs.comment_type }}';
+            const baseBody = `
+              We appreciate your input and will review it soon.
+
+              > [!WARNING]  
+              > A friendly reminder that this is a public forum. Please be cautious when clicking links, downloading files, or running scripts posted by others.
+              >
+              > - Always verify the credibility of links and code.
+              > - Avoid running scripts or installing files from untrusted sources.
+              > - If you're unsure, ask for clarification before proceeding.
+
+              Stay safe and happy SLEAPing!
+
+              Best regards,
+              The Team
+            `;
+            const body = `${{ inputs.body_prefix }}\n\n${baseBody}`;
+
+            const mutation = comment_type === 'discussion'
+              ? `
+                mutation($discussionId: ID!, $body: String!) {
+                  addDiscussionComment(input: {discussionId: $discussionId, body: $body}) {
+                    comment {
+                      id
+                    }
+                  }
+                }
+              `
+              : `
+                mutation($issueId: ID!, $body: String!) {
+                  addComment(input: {subjectId: $issueId, body: $body}) {
+                    commentEdge {
+                      node {
+                        id
+                        body
+                      }
+                    }
+                  }
+                }
+              `;
+
+            const variables = comment_type === 'discussion'
+              ? { discussionId: subject_id, body: body.trim() }
+              : { issueId: subject_id, body: body.trim() };
+
+            await github.graphql(mutation, variables);

.github/workflows/archive/comment.yml

@@ -0,0 +1,24 @@
+name: Comment on New Discussions and Issues
+
+on:
+  discussion:
+    types: [created]
+  issues:
+    types: [opened]
+
+jobs:
+  comment_on_discussion:
+    if: github.event_name == 'discussion'
+    uses: ./.github/workflows/comment-template.yml
+    with:
+      subject_id: ${{ github.event.discussion.node_id }}
+      body_prefix: "Thank you for starting a new discussion!"
+      comment_type: "discussion"
+
+  comment_on_issue:
+    if: github.event_name == 'issues'
+    uses: ./.github/workflows/comment-template.yml
+    with:
+      subject_id: ${{ github.event.issue.node_id }}
+      body_prefix: "Thank you for opening a new issue!"
+      comment_type: "issue"