Merge branch 'main' into configfile_default

simonsobs · Nov 15, 2024 · 0fb045f · 0fb045f
2 parents abaa4cf + 84db894
commit 0fb045f
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Showing 162 changed files with 11,511 additions and 5,212 deletions.
diff --git a/.flake8 b/.flake8
@@ -16,7 +16,7 @@ exclude =
     socs/mibs/MBG-SNMP-ROOT-MIB.py,
     socs/mibs/IBOOTPDU-MIB.py,
     socs/mibs/UPS-MIB.py,
-    versioneer.py,
+    socs/mibs/MBG-SYNCBOX-N2X-MIB.py,
     docs/conf.py,
 per-file-ignores =
     # Windows only dependency

diff --git a/.gitattributes b/.gitattributes
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -3,7 +3,16 @@
 
 version: 2
 updates:
+  - package-ecosystem: "docker"
+    directory: "/"
+    schedule:
+      interval: "daily"
+    reviewers:
+      - "BrianJKoopman"
+
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
       interval: "daily"
+    reviewers:
+      - "BrianJKoopman"
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -29,7 +29,7 @@ jobs:
     # Dockerize
     - name: Build docker images
       run: |
-        docker-compose build
+        docker compose build
 
     - name: Login to Docker Hub
       uses: docker/login-action@v3
@@ -44,13 +44,13 @@ jobs:
         export DOCKER_TAG=`git describe --tags --always`
 
         # Tag all images for upload to the registry
-        docker-compose config | grep 'image: ' | awk -F ': ' '{ print $2 }' | xargs -I {} docker tag {}:latest ${DOCKERHUB_ORG}/{}:latest
-        docker-compose config | grep 'image: ' | awk -F ': ' '{ print $2 }' | xargs -I {} docker tag {}:latest ${DOCKERHUB_ORG}/{}:${DOCKER_TAG}
+        docker compose config | grep 'image: ' | awk -F ': ' '{ print $2 }' | xargs -I {} docker tag {}:latest ${DOCKERHUB_ORG}/{}:latest
+        docker compose config | grep 'image: ' | awk -F ': ' '{ print $2 }' | xargs -I {} docker tag {}:latest ${DOCKERHUB_ORG}/{}:${DOCKER_TAG}
 
         # Upload to docker registry
-        docker-compose config | grep 'image: ' | awk -F ': ' '{ print $2 }' | xargs -I {} docker push ${DOCKERHUB_ORG}/{}:latest
-        docker-compose config | grep 'image: ' | awk -F ': ' '{ print $2 }' | xargs -I {} docker push ${DOCKERHUB_ORG}/{}:${DOCKER_TAG}
-        docker-compose config | grep 'image: ' | awk -F ': ' '{ print $2 }' | xargs -I {} echo ${DOCKERHUB_ORG}/{}:${DOCKER_TAG} pushed
+        docker compose config | grep 'image: ' | awk -F ': ' '{ print $2 }' | xargs -I {} docker push ${DOCKERHUB_ORG}/{}:latest
+        docker compose config | grep 'image: ' | awk -F ': ' '{ print $2 }' | xargs -I {} docker push ${DOCKERHUB_ORG}/{}:${DOCKER_TAG}
+        docker compose config | grep 'image: ' | awk -F ': ' '{ print $2 }' | xargs -I {} echo ${DOCKERHUB_ORG}/{}:${DOCKER_TAG} pushed
 
   wheel:
     name: build and deploy to PyPI
@@ -62,7 +62,7 @@ jobs:
 
     steps:
     - name: Set up Python 3.8
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: 3.8
 

diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml
@@ -10,6 +10,7 @@ on:
       - '.flake8'
       - '.pre-commit-config.yaml'
       - '.readthedocs.yaml'
+      - '.github/dependabot.yml'
 
 jobs:
   test:
@@ -30,7 +31,7 @@ jobs:
     # Dockerize
     - name: Build docker images
       run: |
-        docker-compose build
+        docker compose build
 
     - name: Login to Docker Hub
       uses: docker/login-action@v3
@@ -46,11 +47,11 @@ jobs:
         echo "${DOCKER_TAG}"
 
         # Tag all images for upload to the registry
-        docker-compose config | grep 'image: ' | awk -F ': ' '{ print $2 }' | xargs -I {} docker tag {}:latest ${DOCKERHUB_ORG}/{}:${DOCKER_TAG}
+        docker compose config | grep 'image: ' | awk -F ': ' '{ print $2 }' | xargs -I {} docker tag {}:latest ${DOCKERHUB_ORG}/{}:${DOCKER_TAG}
 
         # Upload to docker registry
-        docker-compose config | grep 'image: ' | awk -F ': ' '{ print $2 }' | xargs -I {} docker push ${DOCKERHUB_ORG}/{}:${DOCKER_TAG}
-        docker-compose config | grep 'image: ' | awk -F ': ' '{ print $2 }' | xargs -I {} echo ${DOCKERHUB_ORG}/{}:${DOCKER_TAG} pushed
+        docker compose config | grep 'image: ' | awk -F ': ' '{ print $2 }' | xargs -I {} docker push ${DOCKERHUB_ORG}/{}:${DOCKER_TAG}
+        docker compose config | grep 'image: ' | awk -F ': ' '{ print $2 }' | xargs -I {} echo ${DOCKERHUB_ORG}/{}:${DOCKER_TAG} pushed
 
   # testing so we can catch any issues before release
   # if issues are found, test locally, or copy to pytest.yml for test on push
@@ -61,7 +62,7 @@ jobs:
 
     steps:
     - name: Set up Python 3.8
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: 3.8
 

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -9,16 +9,18 @@ on:
       - '.flake8'
       - '.pre-commit-config.yaml'
       - '.readthedocs.yaml'
+      - '.github/dependabot.yml'
   workflow_call:
 
 jobs:
   test:
     name: pytest with coverage
     runs-on: ubuntu-latest
+    timeout-minutes: 60
 
     steps:
     - name: Cancel Previous Runs
-      uses: styfle/cancel-workflow-action@0.11.0
+      uses: styfle/cancel-workflow-action@0.12.1
       with:
         access_token: ${{ github.token }}
 
@@ -27,7 +29,7 @@ jobs:
         sudo apt-get install -y socat
 
     - name: Set up Python 3.8
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: 3.8
 
@@ -52,7 +54,7 @@ jobs:
 
     - name: Build docker test images
       run: |
-        docker-compose build socs
+        docker compose build socs
 
     # Integration Tests
     - name: Run integration tests

diff --git a/.github/workflows/skipped-pytest.yml b/.github/workflows/skipped-pytest.yml
@@ -9,6 +9,7 @@ on:
       - '.flake8'
       - '.pre-commit-config.yaml'
       - '.readthedocs.yaml'
+      - '.github/dependabot.yml'
 
 jobs:
   test:

diff --git a/.github/workflows/skipped-test-build.yml b/.github/workflows/skipped-test-build.yml
@@ -9,6 +9,7 @@ on:
       - '.flake8'
       - '.pre-commit-config.yaml'
       - '.readthedocs.yaml'
+      - '.github/dependabot.yml'
 
 jobs:
   build:

diff --git a/.github/workflows/test-build.yml b/.github/workflows/test-build.yml
@@ -9,6 +9,7 @@ on:
       - '.flake8'
       - '.pre-commit-config.yaml'
       - '.readthedocs.yaml'
+      - '.github/dependabot.yml'
 
 jobs:
   build:
@@ -25,4 +26,4 @@ jobs:
     # Dockerize
     - name: Build docker images
       run: |
-        docker-compose build
+        docker compose build
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,6 @@
+# dynamic package version
+socs/_version.py
+
 # iPython Notebooks
 *.ipynb
 

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,21 +1,21 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
     -   id: check-ast
     -   id: check-yaml
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
 -   repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
     - id: isort
       name: isort (python)
 -   repo: https://github.com/hhatto/autopep8
-    rev: v2.0.4
+    rev: v2.3.1
     hooks:
     -   id: autopep8
 -   repo: https://github.com/pycqa/flake8
-    rev: 6.1.0
+    rev: 7.1.1
     hooks:
     -   id: flake8
diff --git a/Dockerfile b/Dockerfile
@@ -2,7 +2,7 @@
 # A container setup with an installation of socs.
 
 # Use the ocs image as a base
-FROM simonsobs/ocs:v0.10.2
+FROM simonsobs/ocs:v0.11.3-3-g63fd5ef
 
 # Set up the cryo/smurf user and group so this can run on smurf-servers
 # See link for how all other smurf-containers are set up:
@@ -16,10 +16,9 @@ RUN useradd -d /home/cryo -M cryo -u 1000 && \
 
 # Install packages
 # suprsync agent - rsync
-# labjack agent - wget, python3-pip, libusb-1.0-0-dev, udev
+# labjack agent - wget, libusb-1.0-0-dev, udev
 RUN apt-get update && apt-get install -y rsync \
     wget \
-    python3-pip \
     libusb-1.0-0-dev \
     udev
 
@@ -35,13 +34,15 @@ RUN ./labjack_ljm_software_2020_03_30_x86_64/labjack_ljm_installer.run -- --no-r
 COPY requirements/ /app/socs/requirements
 COPY requirements.txt /app/socs/requirements.txt
 WORKDIR /app/socs/
-RUN pip3 install -r requirements.txt
+# Work around https://github.com/pypa/setuptools/issues/4483/ temporarily
+RUN python -m pip install -U "setuptools<71.0.0"
+RUN python -m pip install -r requirements.txt
 
 # Copy the current directory contents into the container at /app
 COPY . /app/socs/
 
 # Install socs
-RUN pip3 install .
+RUN python -m pip install .
 
 # Reset workdir to avoid local imports
 WORKDIR /

diff --git a/MANIFEST.in b/MANIFEST.in
diff --git a/README.rst b/README.rst
@@ -2,27 +2,8 @@
 SOCS - Simons Observatory Control System
 ========================================
 
-.. image:: https://img.shields.io/github/actions/workflow/status/simonsobs/socs/develop.yml?branch=main
-    :target: https://github.com/simonsobs/socs/actions?query=workflow%3A%22Build+Test+Images%22
-    :alt: GitHub Workflow Status
-
-.. image:: https://readthedocs.org/projects/socs/badge/?version=main
-    :target: https://socs.readthedocs.io/en/main/?badge=main
-    :alt: Documentation Status
-
-.. image:: https://coveralls.io/repos/github/simonsobs/socs/badge.svg
-    :target: https://coveralls.io/github/simonsobs/socs
-
-.. image:: https://img.shields.io/badge/dockerhub-latest-blue
-    :target: https://hub.docker.com/r/simonsobs/socs
-
-.. image:: https://img.shields.io/pypi/v/socs
-   :target: https://pypi.org/project/socs/
-   :alt: PyPI Package
-
-.. image:: https://results.pre-commit.ci/badge/github/simonsobs/socs/main.svg
-   :target: https://results.pre-commit.ci/latest/github/simonsobs/socs/main
-   :alt: pre-commit.ci status
+| |pypi| |versions| |docker| |license|
+| |tests| |pre-commit| |coverage| |docs|
 
 Overview
 --------
@@ -142,3 +123,33 @@ This project is licensed under the BSD 2-Clause License - see the
 `LICENSE.txt`_ file for details.
 
 .. _LICENSE.txt: https://github.com/simonsobs/socs/blob/main/LICENSE.txt
+
+
+.. |coverage| image:: https://coveralls.io/repos/github/simonsobs/socs/badge.svg
+    :target: https://coveralls.io/github/simonsobs/socs
+
+.. |docker| image:: https://img.shields.io/badge/dockerhub-latest-blue
+    :target: https://hub.docker.com/r/simonsobs/socs
+
+.. |docs| image:: https://readthedocs.org/projects/socs/badge/?version=main
+    :target: https://socs.readthedocs.io/en/main/?badge=main
+    :alt: Documentation Status
+
+.. |license| image:: https://img.shields.io/pypi/l/socs
+    :target: LICENSE.txt
+    :alt: PyPI - License
+
+.. |pre-commit| image:: https://results.pre-commit.ci/badge/github/simonsobs/socs/main.svg
+   :target: https://results.pre-commit.ci/latest/github/simonsobs/socs/main
+   :alt: pre-commit.ci status
+
+.. |pypi| image:: https://img.shields.io/pypi/v/socs
+   :target: https://pypi.org/project/socs/
+   :alt: PyPI Package
+
+.. |tests| image:: https://github.com/simonsobs/socs/actions/workflows/develop.yml/badge.svg?branch=main
+    :target: https://github.com/simonsobs/socs/actions/workflows/develop.yml
+    :alt: GitHub Workflow Status
+
+.. |versions| image:: https://img.shields.io/pypi/pyversions/socs
+    :alt: PyPI - Python Version
diff --git a/docker/pysmurf_controller/Dockerfile b/docker/pysmurf_controller/Dockerfile
@@ -1,4 +1,4 @@
-FROM simonsobs/sodetlib:v0.5.2
+FROM simonsobs/sodetlib:v0.5.2-20-gdd529b5
 
 ENV OCS_CONFIG_DIR /config
 

diff --git a/docker/wiregrid_actuator/Dockerfile b/docker/wiregrid_actuator/Dockerfile
@@ -2,23 +2,28 @@ FROM socs:latest
 
 WORKDIR /home/ocs/
 
+# This line is to avoid warnings during the build.
+ENV DEBIAN_FRONTEND="noninteractive"
+
+# Galil installation information:
+# -https://www.galil.com/sw/pub/all/doc/global/install/linux/ubuntu/
+# -https://www.galil.com/sw/pub/all/doc/gclib/html/python.html
 RUN apt-get update \
  && apt-get install -y apt-utils \
  && apt-get install -y wget libavahi-common-dev libavahi-client-dev libavahi-core-dev libcap-dev libdaemon-dev avahi-daemon \
- && wget http://www.galil.com/sw/pub/all/crypto/GALIL-GPG-KEY-E29D0E4B.asc \
- && apt-key add GALIL-GPG-KEY-E29D0E4B.asc \
- && wget http://www.galil.com/sw/pub/ubuntu/20.04/galil.list \
- && cp galil.list /etc/apt/sources.list.d \
+ && wget https://www.galil.com/sw/pub/apt/all/galil-release_1_all.deb \
+ && apt-get install -y ./galil-release_1_all.deb \
+ && rm ./galil-release_1_all.deb \
  && apt-get update \
- && apt-get install -y --download-only gclib \
- && dpkg -x $(find / -name "gclib*.deb") / \
- && apt-get install -y gclib \
+ && apt install -y gclib \
  && apt-get install -y --download-only gcapsd \
  && dpkg -x $(find / -name "gcapsd*.deb") /tmp/gcapsd/ \
- && mv /tmp/gcapsd/usr/sbin/gcapsd /usr/sbin/ \
+ && mv -v /tmp/gcapsd/usr/sbin/gcapsd /usr/sbin/ \
  && rm -r /tmp/gcapsd/ \
- && tar -xvf /usr/share/doc/gclib/src/gclib_python.tar.gz \
- && python3 setup.py install
+ && cp /usr/share/gclib/src/wrappers/python/* . \
+ && cp /usr/share/gclib/doc/examples/python/* . \
+ && python3 -m pip install . \
+ && python3 -c "import gclib; print(f'gclib location: {gclib.__file__}')"
 
 COPY . .