Merge pull request #117 from simonsobs/develop

Release v0.1.0

.github/workflows/develop.yml

@@ -13,8 +13,12 @@ jobs:
       # Fetch all history for all tags and branches
       with:
         fetch-depth: 0
+    - name: Set up Python 3.8 
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8 
 
-    # Test
+    # Test (steps from pytest workflow)
     - name: Build docker images
       run: |
         docker-compose build
@@ -23,6 +27,19 @@ jobs:
       run: |
         docker run -v $PWD:/coverage --rm socs sh -c "COVERAGE_FILE=/coverage/.coverage.docker python3 -m pytest -p no:wampy --cov /app/socs/socs/ ./tests/"
 
+    - name: Report test coverage
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        pip install coveralls
+        coverage combine
+        coverage report
+        coveralls
+
+    - name: Test documentation build
+      run: |
+        docker run --rm socs sh -c "make -C docs/ html"
+
     # Dockerize
     - name: Build and push development docker image
       env:

.github/workflows/official-docker-images.yml

@@ -13,16 +13,25 @@ jobs:
       # Fetch all history for all tags and branches
       with:
         fetch-depth: 0
+    - name: Set up Python 3.8 
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8 
 
-    # Test
+    # Build
     - name: Build docker images
       run: |
         docker-compose build
 
+    # Test (already been run by pytest workflow, but they don't take long...)
     - name: Test with pytest wtihin a docker container
       run: |
         docker run -v $PWD:/coverage --rm socs sh -c "COVERAGE_FILE=/coverage/.coverage.docker python3 -m pytest -p no:wampy --cov /app/socs/socs/ ./tests/"
 
+    - name: Test documentation build
+      run: |
+        docker run --rm socs sh -c "make -C docs/ html"
+
     # Dockerize
     - name: Build and push official docker image
       env:

.github/workflows/pytest.yml

@@ -0,0 +1,38 @@
+name: Run Tests
+
+on:
+  push:
+    branches-ignore: [ develop ]
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-18.04
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+
+    - name: Build docker images
+      run: |
+        docker-compose build
+
+    - name: Test with pytest wtihin a docker container
+      run: |
+        docker run -v $PWD:/coverage --rm socs sh -c "COVERAGE_FILE=/coverage/.coverage.docker python3 -m pytest -p no:wampy --cov /app/socs/socs/ ./tests/"
+
+    - name: Report test coverage
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        pip install coveralls
+        coverage combine
+        coverage report
+        coveralls
+
+    - name: Test documentation build
+      run: |
+        docker run --rm socs sh -c "make -C docs/ html"

Dockerfile

@@ -2,7 +2,7 @@
 # A container setup with an installation of socs.
 
 # Use the ocs image as a base
-FROM simonsobs/ocs:v0.6.0-67-g5993b6a-dev
+FROM simonsobs/ocs:v0.7.1
 
 # Copy the current directory contents into the container at /app
 COPY . /app/socs/

README.rst

@@ -2,8 +2,9 @@
 SOCS - Simons Observatory Control System
 ========================================
 
-.. image:: https://travis-ci.com/simonsobs/socs.svg?branch=master
-    :target: https://travis-ci.com/simonsobs/socs
+.. image:: https://img.shields.io/github/workflow/status/simonsobs/socs/Build%20Develop%20Images
+    :target: https://github.com/simonsobs/socs/actions?query=workflow%3A%22Build+Develop+Images%22
+    :alt: GitHub Workflow Status
 
 .. image:: https://readthedocs.org/projects/socs/badge/?version=latest
     :target: https://socs.readthedocs.io/en/latest/?badge=latest

agents/bluefors/Dockerfile

@@ -11,7 +11,7 @@ WORKDIR /app/socs/agents/bluefors/
 COPY . .
 
 # Run registry on container startup
-ENTRYPOINT ["python3", "-u", "bluefors_log_tracker.py"]
+ENTRYPOINT ["dumb-init", "python3", "-u", "bluefors_log_tracker.py"]
 
 # Sensible default instance-id
 CMD ["--instance-id=bluefors"]

agents/bluefors/bluefors_log_tracker.py

@@ -128,11 +128,13 @@ def __init__(self, tracker):
                                     'tc400errorcode_2', 'tc400ovtempelec_2',
                                     'tc400ovtemppump_2', 'tc400setspdatt_2',
                                     'tc400pumpaccel_2', 'tc400commerr_2',
+                                    'nxdsf', 'nxdsct', 'nxdst', 'nxdsbs', 'nxdstrs',
                                     'ctrl_pres', 'cpastate', 'cparun', 'cpawarn',
                                     'cpaerr', 'cpatempwi', 'cpatempwo', 'cpatempo',
                                     'cpatemph', 'cpalp', 'cpalpa', 'cpahp', 'cpahpa',
                                     'cpadp', 'cpacurrent', 'cpahours', 'cpapscale',
-                                    'cpatscale', 'cpasn', 'cpamodel'],
+                                    'cpascale', 'cpatscale', 'cpasn', 'cpamodel',
+                                    'ctrl_pres_ok', 'ctr_pressure_ok'],
                          'heater': ["a1_u", "a1_r_lead", "a1_r_htr", "a2_u",
                                     "a2_r_lead", "a2_r_htr", "htr", "htr_range"]}
 
@@ -235,6 +237,11 @@ def _parse_multi_value_log(self, new_line, log_type, log_name):
         for pattern in self.patterns[log_type]:
             regex = re.compile(rf'{pattern},([0-9\.\+\-E]+)')
             m = regex.search(new_line)
+
+            # skip patterns that don't exist in this log
+            if not m:
+                continue
+
             if log_type == 'channels':
                 data_array[pattern.replace('-', '_')] = int(m.group(1))
             else:

agents/cryomech_cpa/Dockerfile

@@ -15,7 +15,7 @@ COPY . /app/socs/agents/cryomech-cpa/
 
 # Run agent on container startup
 
-ENTRYPOINT ["python3", "-u", "cryomech_cpa_agent.py"]
+ENTRYPOINT ["dumb-init", "python3", "-u", "cryomech_cpa_agent.py"]
 
-CMD ["--site-hub=ws://sisock-crossbar:8001/ws", \
-     "--site-http=http://sisock-crossbar:8001/call"]
+CMD ["--site-hub=ws://crossbar:8001/ws", \
+     "--site-http=http://crossbar:8001/call"]

agents/labjack/Dockerfile

@@ -9,10 +9,23 @@ WORKDIR /app/socs/agents/labjack/
 
 ## Copy this agent into the app/agents directory
 COPY . .
+RUN pip3 install -r requirements.txt
+
+# Install ljm module from labjack, copied from the labjack ljm dockerfile 
+# located at https://hub.docker.com/r/labjack/ljm/dockerfile
+RUN apt-get update
+RUN apt-get install -y wget python3-pip libusb-1.0-0-dev udev
+
+RUN wget https://labjack.com/sites/default/files/software/labjack_ljm_minimal_2020_03_30_x86_64_beta.tar.gz
+RUN tar zxf ./labjack_ljm_minimal_2020_03_30_x86_64_beta.tar.gz
+RUN ./labjack_ljm_minimal_2020_03_30_x86_64/labjack_ljm_installer.run -- --no-restart-device-rules
+
+RUN pip3 install --no-cache-dir https://labjack.com/sites/default/files/software/Python_LJM_2019_04_03.zip
+
 
 # Run registry on container startup
-ENTRYPOINT ["python3", "-u", "labjack_agent.py"]
+ENTRYPOINT ["dumb-init", "python3", "-u", "labjack_agent.py"]
 
 # Sensible default arguments
-CMD ["--site-hub=ws://sisock-crossbar:8001/ws", \
-     "--site-http=http://sisock-crossbar:8001/call"]
+CMD ["--site-hub=ws://crossbar:8001/ws", \
+     "--site-http=http://crossbar:8001/call"]

agents/labjack/labjack_agent.py

@@ -152,7 +152,7 @@ def __init__(self, agent, ip_address, active_channels, function_file,
         if active_channels == 'T7-all':
             self.sensors = ['Channel_{}'.format(i+1) for i in range(14)]
         elif active_channels == 'T4-all':
-            self.sensors = ['Channel_{}'.format(i+1) for i in range(12)]    
+            self.sensors = ['Channel_{}'.format(i+1) for i in range(12)]
         else:
             self.sensors = ['Channel_{}'.format(ch) for ch in active_channels]
         self.ljf = LabJackFunctions()
@@ -167,6 +167,7 @@ def __init__(self, agent, ip_address, active_channels, function_file,
                                               function_file)
             with open(function_file_path, 'r') as stream:
                 self.functions = yaml.safe_load(stream)
+                print(f"Applying conversion functions: {self.functions}")
 
         self.initialized = False
         self.take_data = False

agents/labjack/requirements.txt

@@ -0,0 +1,2 @@
+numexpr
+scipy

agents/lakeshore240/Dockerfile

@@ -11,7 +11,7 @@ WORKDIR /app/socs/agents/lakeshore240/
 COPY . .
 
 # Run registry on container startup
-ENTRYPOINT ["python3", "-u", "LS240_agent.py"]
+ENTRYPOINT ["dumb-init", "python3", "-u", "LS240_agent.py"]
 
-CMD ["--site-hub=ws://sisock-crossbar:8001/ws", \
-     "--site-http=http://sisock-crossbar:8001/call"]
+CMD ["--site-hub=ws://crossbar:8001/ws", \
+     "--site-http=http://crossbar:8001/call"]

agents/lakeshore240/LS240_agent.py

@@ -193,6 +193,21 @@ def start_acq(self, session, params=None):
 
         Method to start data acquisition process.
 
+        The most recent data collected is stored in session.data in the
+        structure::
+
+            >>> session.data
+            {"fields":
+                {"Channel_1": {"T": 99.26, "V": 99.42},
+                 "Channel_2": {"T": 99.54, "V": 101.06},
+                 "Channel_3": {"T": 100.11, "V":100.79},
+                 "Channel_4": {"T": 98.49, "V": 100.77},
+                 "Channel_5": {"T": 97.75, "V": 101.45},
+                 "Channel_6": {"T": 99.58, "V": 101.75},
+                 "Channel_7": {"T": 98.03, "V": 100.82},
+                 "Channel_8": {"T": 101.14, "V":101.01}},
+             "timestamp":1601925677.6914878}
+
         Args:
             sampling_frequency (float):
                 Sampling frequency for data collection. Defaults to 2.5 Hz
@@ -218,20 +233,34 @@ def start_acq(self, session, params=None):
 
             self.take_data = True
 
+            session.data = {"fields": {}}
+
             while self.take_data:
+                current_time = time.time()
                 data = {
-                    'timestamp': time.time(),
+                    'timestamp': current_time,
                     'block_name': 'temps',
                     'data': {}
                 }
 
                 for chan in self.module.channels:
+                    # Read sensor on channel
                     chan_string = "Channel_{}".format(chan.channel_num)
-                    data['data'][chan_string + '_T'] = chan.get_reading(unit='K')
-                    data['data'][chan_string + '_V'] = chan.get_reading(unit='S')
+                    temp_reading = chan.get_reading(unit='K')
+                    sensor_reading = chan.get_reading(unit='S')
+
+                    # For data feed
+                    data['data'][chan_string + '_T'] = temp_reading
+                    data['data'][chan_string + '_V'] = sensor_reading
+
+                    # For session.data
+                    field_dict = {chan_string: {"T": temp_reading, "V": sensor_reading}}
+                    session.data['fields'].update(field_dict)
 
                 self.agent.publish_to_feed('temperatures', data)
 
+                session.data.update({'timestamp': current_time})
+
                 time.sleep(sleep_time)
 
             self.agent.feeds['temperatures'].flush_buffer()

agents/lakeshore372/Dockerfile

@@ -11,8 +11,8 @@ WORKDIR /app/socs/agents/lakeshore372/
 COPY . .
 
 # Run registry on container startup
-ENTRYPOINT ["python3", "-u", "LS372_agent.py"]
+ENTRYPOINT ["dumb-init", "python3", "-u", "LS372_agent.py"]
 
 # Sensible default arguments
-CMD ["--site-hub=ws://sisock-crossbar:8001/ws", \
-     "--site-http=http://sisock-crossbar:8001/call"]
+CMD ["--site-hub=ws://crossbar:8001/ws", \
+     "--site-http=http://crossbar:8001/call"]