use pyproj.toml, src layout

.coveragerc

@@ -1,5 +1,23 @@
 [run]
-omit = */tests/*
+omit =
+    */tests/*
+    */docs/*
+    setup.py
+source =
+    hera_mc
 
 [report]
-omit = */tests/*
+omit =
+    */tests/*
+    */docs/*
+    setup.py
+
+show_missing = true
+
+[paths]
+source =
+    src
+    */site-packages
+tests =
+    tests
+    */tests

.github/workflows/testsuite.yml

@@ -27,7 +27,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
     services:
       postgres:
         image: postgres:10.8
@@ -52,7 +52,7 @@ jobs:
     steps:
       - uses: actions/checkout@master
         with:
-          fetch-depth: 1
+          fetch-depth: 0
 
       - name: Setup Miniforge
         uses: conda-incubator/setup-miniconda@v3
@@ -73,7 +73,7 @@ jobs:
 
       - name: Install
         run: |
-          pip install --no-deps .
+          pip install --no-deps -e .
 
       - name: Setup postgres
         run: |
@@ -100,7 +100,7 @@ jobs:
           DOCKER_NAME=`/usr/bin/docker ps -a --filter="ancestor=redis" --format='{{.Names}}'`
           /usr/bin/docker stop $DOCKER_NAME
           sudo rm /data/dump.rdb
-          sudo cp hera_mc/data/test_data/dump.rdb /data
+          sudo cp src/hera_mc/data/test_data/dump.rdb /data
           /usr/bin/docker start $DOCKER_NAME
           DOCKER_IP=`docker inspect -f '{{range .NetworkSettings.Networks}}{{.IPAddress}}{{end}}' $DOCKER_NAME`
           echo "$DOCKER_IP redishost" | sudo tee -a /etc/hosts
@@ -111,16 +111,21 @@ jobs:
         env:
           POSTGRES_PORT: ${{ job.services.postgres.ports[5432] }} # get randomly assigned published port
 
-      - uses: codecov/codecov-action@v1.5.2
-        if: matrix.os == 'ubuntu-latest' && success()
+      - name: check coverage report
+        run: |
+          ls
+          cat coverage.xml
+
+      - uses: codecov/codecov-action@v5
+        if: success()
         with:
           token: ${{secrets.CODECOV_TOKEN}} #required
-          file: ./coverage.xml #optional
+          files: ./coverage.xml #optional
 
   min_deps:
     env:
       ENV_NAME: min_deps
-      PYTHON: "3.11"
+      PYTHON: "3.12"
       WITH_SUDO: yes
       # use localhost for the host here because we are running the job on the VM.
       POSTGRES_HOST: localhost
@@ -152,7 +157,7 @@ jobs:
     steps:
       - uses: actions/checkout@master
         with:
-          fetch-depth: 1
+          fetch-depth: 0
 
       - name: Setup Miniforge
         uses: conda-incubator/setup-miniconda@v3
@@ -194,18 +199,20 @@ jobs:
 
       - name: Run Tests
         run: |
-          mkdir -p empty
-          cd empty
-          pytest --pyargs hera_mc --cov=hera_mc --cov-config=../.coveragerc --cov-report xml:../coverage.xml --junitxml=../test-reports/xunit.xml
-          cd ..
+          python -m pytest --cov=hera_mc --cov-config=.coveragerc --cov-report xml:./coverage.xml --junitxml=test-reports/xunit.xml
         env:
           POSTGRES_PORT: ${{ job.services.postgres.ports[5432] }} # get randomly assigned published port
 
-      - uses: codecov/codecov-action@v1.5.2
+      - name: check coverage report
+        run: |
+          ls
+          cat coverage.xml
+
+      - uses: codecov/codecov-action@v5
         if: success()
         with:
           token: ${{secrets.CODECOV_TOKEN}} #required
-          file: ./coverage.xml #optional
+          files: ./coverage.xml #optional
 
   min_versions:
     env:
@@ -238,11 +245,18 @@ jobs:
         - 5432:5432
         # needed because the postgres container does not provide a healthcheck
         options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
+      redis:
+        image: redis
+        env:
+          REDIS_HOST: redishost
+        ports:
+        - 6379:6379
+        options: --entrypoint redis-server --network-alias $REDIS_HOST -v /data:/data --health-cmd "redis-cli ping" --health-interval 10s --health-timeout 5s --health-retries 5
 
     steps:
       - uses: actions/checkout@master
         with:
-          fetch-depth: 1
+          fetch-depth: 0
 
       - name: Setup Miniforge
         uses: conda-incubator/setup-miniconda@v3
@@ -282,20 +296,35 @@ jobs:
         env:
           POSTGRES_PORT: ${{ job.services.postgres.ports[5432] }} # get randomly assigned published port
 
+      - name: Initialize Redis
+        # Grab the name of the redis container with bash magic
+        # stop the container, replace the dump file with our save file
+        # add the IP to the hosts file to preserve some hardcoded defaults
+        run: |
+          DOCKER_NAME=`/usr/bin/docker ps -a --filter="ancestor=redis" --format='{{.Names}}'`
+          /usr/bin/docker stop $DOCKER_NAME
+          sudo rm /data/dump.rdb
+          sudo cp src/hera_mc/data/test_data/dump.rdb /data
+          /usr/bin/docker start $DOCKER_NAME
+          DOCKER_IP=`docker inspect -f '{{range .NetworkSettings.Networks}}{{.IPAddress}}{{end}}' $DOCKER_NAME`
+          echo "$DOCKER_IP redishost" | sudo tee -a /etc/hosts
+
       - name: Run Tests
         run: |
-          mkdir -p empty
-          cd empty
-          pytest --pyargs hera_mc --cov=hera_mc --cov-config=../.coveragerc --cov-report xml:../coverage.xml --junitxml=../test-reports/xunit.xml
-          cd ..
+          python -m pytest --cov=hera_mc --cov-config=.coveragerc --cov-report xml:./coverage.xml --junitxml=test-reports/xunit.xml
         env:
           POSTGRES_PORT: ${{ job.services.postgres.ports[5432] }} # get randomly assigned published port
 
-      - uses: codecov/codecov-action@v1.5.2
+      - name: check coverage report
+        run: |
+          ls
+          cat coverage.xml
+
+      - uses: codecov/codecov-action@v5
         if: success()
         with:
           token: ${{secrets.CODECOV_TOKEN}} #required
-          file: ./coverage.xml #optional
+          files: ./coverage.xml #optional
 
   warning_tests:
     env:
@@ -360,7 +389,7 @@ jobs:
 
       - name: Install
         run: |
-          pip install --no-deps .
+          pip install --no-deps -e .
 
       - name: Setup postgres
         run: |
@@ -387,13 +416,24 @@ jobs:
           DOCKER_NAME=`/usr/bin/docker ps -a --filter="ancestor=redis" --format='{{.Names}}'`
           /usr/bin/docker stop $DOCKER_NAME
           sudo rm /data/dump.rdb
-          sudo cp hera_mc/data/test_data/dump.rdb /data
+          sudo cp src/hera_mc/data/test_data/dump.rdb /data
           /usr/bin/docker start $DOCKER_NAME
           DOCKER_IP=`docker inspect -f '{{range .NetworkSettings.Networks}}{{.IPAddress}}{{end}}' $DOCKER_NAME`
           echo "$DOCKER_IP redishost" | sudo tee -a /etc/hosts
 
       - name: Run Tests
         run: |
-          python -m pytest -W error
+          python -m pytest -W error --cov=hera_mc --cov-config=.coveragerc --cov-report xml:./coverage.xml --junitxml=test-reports/xunit.xml
         env:
           POSTGRES_PORT: ${{ job.services.postgres.ports[5432] }} # get randomly assigned published port
+
+      - name: check coverage report
+        run: |
+          ls
+          cat coverage.xml
+
+      - uses: codecov/codecov-action@v5
+        if: success()
+        with:
+          token: ${{secrets.CODECOV_TOKEN}} #required
+          files: ./coverage.xml #optional

.gitignore

@@ -88,4 +88,4 @@ target/
 hera_mc/GIT_INFO
 .pytest_cache
 
-hera_mc/data/test_data/hera_mc_test.db
+src/hera_mc/data/test_data/hera_mc_test.db

README.md

@@ -1,8 +1,8 @@
 hera_mc
 =======
 
-![](https://github.com/HERA-Team/hera_mc/workflows/Run%20Tests/badge.svg?branch=master)
-[![codecov](https://codecov.io/gh/HERA-Team/hera_mc/branch/master/graph/badge.svg)](https://codecov.io/gh/HERA-Team/hera_mc)
+![](https://github.com/HERA-Team/hera_mc/actions/workflows/testsuite.yml/badge.svg?branch=main)
+[![codecov](https://codecov.io/gh/HERA-Team/hera_mc/branch/main/graph/badge.svg)](https://codecov.io/gh/HERA-Team/hera_mc)
 
 This is the main repository for HERA's monitor and control subsystems.
 
@@ -52,10 +52,10 @@ The required dependencies are:
 - cartopy >=0.21
 - numpy >= 1.23
 - psycopg>=3.2.2
-- pyuvdata >= 2.2.9
+- pyuvdata >= 2.3.0
 - pyyaml >= 5.4.1
 - redis-py >= 4.3.4 (Note that this is called "redis" on pypi and "redis-py" on conda)
-- setuptools_scm <7.0|>=7.0.3
+- setuptools_scm >= 8.1
 - sqlalchemy >= 2.0
 
 the optional dependencies are:

alembic/env.py

@@ -18,6 +18,7 @@
 db_data = config_data.get("databases")
 db_data = db_data.get(db_name)
 db_url = db_data.get("url")
+# Add "+psycopg" to the url to ensure sqlalchemy uses the right psycopg package
 if "postgresql" in db_url and "postgresql+psycopg" not in db_url:
     db_url = db_url.replace("postgresql", "postgresql+psycopg")
 config.set_main_option("sqlalchemy.url", db_url)

ci/example_config.json

@@ -14,7 +14,7 @@
       "mode": "testing"
     },
     "sqlite_testing":{
-      "url": "sqlite:///~/hera_mc/data/test_data/hera_mc_test.db",
+      "url": "sqlite:///~/src/hera_mc/data/test_data/hera_mc_test.db",
       "mode": "testing"
     }
   }

ci/min_deps.yaml

@@ -10,8 +10,8 @@ dependencies:
   - psycopg>=3.2.2
   - pytest>=6.2.5
   - pytest-cov
-  - pyuvdata>=2.2.9
+  - pyuvdata>=2.3.0
   - pyyaml>=5.4.1
   - redis-py>=4.3.4
-  - setuptools_scm<7.0|>=7.0.3
+  - setuptools_scm>=8.1
   - sqlalchemy>=2.0

ci/min_versions.yaml

@@ -16,10 +16,10 @@ dependencies:
   - pytest==6.2.5
   - pytest-cov
   - python-dateutil==2.8.2
-  - pyuvdata==2.2.9
+  - pyuvdata==2.3.0
   - pyyaml==5.4.1
   - redis-py==4.3.4
-  - setuptools_scm<7.0
+  - setuptools_scm==8.1
   - sqlalchemy==2.0.0
   - tabulate==0.8.10
   - pip:

ci/publish.yml

@@ -7,10 +7,10 @@ dependencies:
   - cartopy>=0.21.0
   - numpy>=1.23.*
   - psycopg>=3.2.2
-  - pyuvdata>=2.2.9
+  - pyuvdata>=2.3.0
   - pyyaml>=5.4.1
   - redis-py>=4.3.4
-  - setuptools_scm<7.0|>=7.0.3
+  - setuptools_scm>=8.1
   - sqlalchemy>=2.0
   - pip
   - pip:

ci/tests.yaml

@@ -16,10 +16,10 @@ dependencies:
   - pytest>=6.2.5
   - pytest-cov
   - python-dateutil>=2.8.2
-  - pyuvdata>=2.2.9
+  - pyuvdata>=2.3.0
   - pyyaml>=5.4.1
   - redis-py>=4.3.4
-  - setuptools_scm<7.0|>=7.0.3
+  - setuptools_scm>=8.1
   - sqlalchemy>=2.0
   - tabulate>=0.8.10
   - tornado>=6.2

environment.yaml

@@ -16,10 +16,10 @@ dependencies:
   - pytest>=6.2.5
   - pytest-cov
   - python-dateutil>=2.8.2
-  - pyuvdata>=2.2.9
+  - pyuvdata>=2.3.0
   - pyyaml>=5.4.1
   - redis-py>=4.3.4
-  - setuptools_scm<7.0|>=7.0.3
+  - setuptools_scm>=8.1
   - sqlalchemy>=1.4.0
   - tabulate>=0.8.10
   - tornado>=6.2