Merge pull request #1495 from AllenNeuralDynamics/dev

Release v2.0.0 (merge into main)

Author: dbirman

.github/workflows/publish_dev.yml

@@ -20,10 +20,10 @@ jobs:
       - uses: actions/checkout@master
       - name: Pull latest changes
         run: git pull origin dev
-      - name: Set up Python 3.8
+      - name: Set up Python 3.10
         uses: actions/setup-python@v3
         with:
-          python-version: 3.8
+          python-version: '3.10'
       - name: Configure aws credentials
         uses: aws-actions/configure-aws-credentials@v2
         with:

.github/workflows/run_dev_tests.yml

@@ -29,7 +29,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.8', '3.9', '3.10', '3.11' ]
+        python-version: [ '3.10', '3.11', '3.12', '3.13' ]
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}

.github/workflows/run_main_tests.yml

@@ -31,7 +31,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.8', '3.9', '3.10', '3.11' ]
+        python-version: [ '3.10', '3.11', '3.12', '3.13' ]
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}

.github/workflows/tag_and_publish_main.yml

@@ -53,10 +53,10 @@ jobs:
       - uses: actions/checkout@master
       - name: Pull latest changes
         run: git pull origin main
-      - name: Set up Python 3.8
+      - name: Set up Python 3.10
         uses: actions/setup-python@v3
         with:
-          python-version: 3.8
+          python-version: '3.10'
       - name: Configure aws credentials
         uses: aws-actions/configure-aws-credentials@v2
         with:
@@ -69,40 +69,3 @@ jobs:
           python -m aind_data_schema.utils.json_writer --output $TEMP_DIR --attach-version
           python -m pip install awscli
           aws s3 sync $TEMP_DIR s3://${AWS_DATA_SCHEMA_BUCKET}/$S3_PREFIX
-
-  upload_diagrams:
-    needs: tag_and_publish
-    runs-on: ubuntu-latest
-    permissions:
-      id-token: write
-      contents: read
-    env:
-      AWS_DATA_SCHEMA_ROLE: ${{ secrets.AWS_DATA_SCHEMA_ROLE_PROD }}
-      AWS_DATA_SCHEMA_BUCKET: ${{ vars.AWS_DATA_SCHEMA_BUCKET_PROD }}
-      AWS_REGION : ${{ vars.AWS_REGION_PROD }}
-      DIAGRAM_DIRECTORY: ./docs/source/_static/diagrams
-    steps:
-      - uses: actions/checkout@master
-      - name: Pull latest changes
-        run: git pull origin main
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v3
-        with:
-          python-version: 3.8
-      - name: Install dependencies
-        run: |
-          sudo apt install graphviz libgraphviz-dev -y
-          python -m pip install -e .[docs] --no-cache-dir
-          python -m pip install awscli
-      - name: Generate erdantic diagrams
-        run: |
-          mkdir $DIAGRAM_DIRECTORY
-          python -m aind_data_schema.utils.diagrams $DIAGRAM_DIRECTORY
-      - name: Configure aws credentials
-        uses: aws-actions/configure-aws-credentials@v2
-        with:
-          role-to-assume: ${{ env.AWS_DATA_SCHEMA_ROLE }}
-          role-session-name: github-diagram-upload-session
-          aws-region: ${{ env.AWS_REGION }}
-      - name: Create and upload diagrams
-        run: aws s3 sync $DIAGRAM_DIRECTORY s3://${AWS_DATA_SCHEMA_BUCKET}/diagrams

.github/workflows/update_docs.yml

@@ -14,10 +14,10 @@ jobs:
       - uses: actions/checkout@v3
         with:
           token: ${{ secrets.SERVICE_TOKEN }}
-      - name: Set up Python 3.8
+      - name: Set up Python 3.10
         uses: actions/setup-python@v3
         with:
-          python-version: 3.8
+          python-version: '3.10'
       - name: Install dependencies
         run: |
           python -m pip install -e .[dev] --no-cache-dir
@@ -51,10 +51,10 @@ jobs:
       - uses: actions/checkout@v3
         with:
           token: ${{ secrets.SERVICE_TOKEN }}
-      - name: Set up Python 3.8
+      - name: Set up Python 3.10
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: '3.10'
       - name: Install dependencies
         run: |
           sudo apt install graphviz libgraphviz-dev -y

.gitignore

@@ -140,3 +140,8 @@ dmypy.json
 
 # Jupyter
 notebook/
+*.vscode
+ephys_instrument.json
+examples/*.json
+*.json
+docs/base/models/*

.readthedocs.yaml

@@ -3,7 +3,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.8"
+    python: "3.13"
 
 python:
   install:
@@ -12,3 +12,7 @@ python:
       extra_requirements:
         - dev
         - docs
+
+sphinx:
+  # Path to your Sphinx configuration file.
+  configuration: docs/source/conf.py

CODE_OF_CONDUCT.md

@@ -0,0 +1,133 @@
+
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official email address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[email protected].
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+[https://www.contributor-covenant.org/version/2/0/code_of_conduct.html][v2.0].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available
+at [https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.0]: https://www.contributor-covenant.org/version/2/0/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations