Merge pull request #108 from ratt-ru/deps-update

Dependancy and deployment update

.github/workflows/ci.yml

@@ -2,33 +2,51 @@ name: Ubuntu CI
 
 on: [push, pull_request]
 
+env:
+  POETRY_VERSION: 1.4.0
+
 jobs:
   test:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.6", "3.7", "3.8"]
-
+        os: [ ubuntu-20.04, ubuntu-22.04 ]
+        python-version: ["3.8", "3.9", "3.10"]
     steps:
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
+      - name: Cache Installations
+        id: cache-installs
+        uses: actions/cache@v3
+        with:
+          path: ~/.local
+          key: install-${{ env.INSTALL_CACHE_HASH }}-2
+
+      - name: Install Poetry
+        if: steps.cache-installs.outputs.cache-hit != 'true'
+        run: |
+          curl -sSL https://install.python-poetry.org | python3 - --version ${{ env.POETRY_VERSION }}
+
+      - name: Test poetry
+        run: poetry --version
+
       - name: Checkout source
         uses: actions/checkout@v2
         with:
           fetch-depth: 1
 
-      - name: Install latest versions of pip, setuptools and wheel
-        run: python -m pip install -U pip setuptools wheel
-
       - name: Install shadems
-        run: pip install -e .[testing]
+        run: poetry install --extras "testing"
+
+      - name: Test command
+        run: poetry run python bin/shadems --help
 
       - name: Run testsuite
-        run: py.test shade_ms/
+        run: poetry run py.test -vvv shade_ms/
 
   # deploy:
   #   needs: [test]
@@ -72,4 +90,4 @@ jobs:
   #       if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
   #       with:
   #         user: __token__
-  #         password: ${{ secrets.pypi_token }}
+  #         password: ${{ secrets.pypi_token }}

.github/workflows/publish_package.yml

@@ -4,6 +4,9 @@ on:
   release:
     types: [published]
 
+env:
+  POETRY_VERSION: 1.4.0
+
 jobs:
   deploy:
 
@@ -12,17 +15,37 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
-    - name: Install dependencies
+
+    - name: Cache Installations
+      id: cache-installs
+      uses: actions/cache@v3
+      with:
+        path: ~/.local
+        key: install-${{ env.INSTALL_CACHE_HASH }}-2
+
+    - name: Install Poetry
+      if: steps.cache-installs.outputs.cache-hit != 'true'
       run: |
-        python -m pip install --upgrade pip
-        pip install build
-    - name: Build package
-      run: python -m build
-    - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+        curl -sSL https://install.python-poetry.org | python3 - --version ${{ env.POETRY_VERSION }}
+    - name: Test poetry
+      run: poetry --version
+
+    - name: Checkout source
+      uses: actions/checkout@v2
+      with:
+        fetch-depth: 1
+
+    - name: Install shadems
+      run: poetry install
+
+    - name: Build distribution
+      run: poetry build
+
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@master
       with:
         user: __token__
         password: ${{ secrets.PYPI_API_TOKEN }}

pyproject.toml

@@ -0,0 +1,45 @@
+[tool.poetry]
+name = "shadems"
+version = "0.5.2"
+description = "Rapid Measurement Set plotting with dask-ms and datashader"
+authors = ["Ian Heywood & RATT <ian.heywood@physics.ox.ac.uk>"]
+license = "GPL-2.0-only"
+homepage = "https://github.com/ratt-ru/shadeMS"
+repository = "https://github.com/ratt-ru/shadeMS"
+readme = "README.md"
+keywords = ["Astronomy", "Visualisation", "Packaging"]
+classifiers = [
+        "Development Status :: 4 - Beta",
+        "Intended Audience :: Science/Research",
+        "License :: OSI Approved :: GNU General Public License v2 (GPLv2)",
+        "Operating System :: POSIX :: Linux",
+        "Programming Language :: Python",
+        "Topic :: Scientific/Engineering :: Astronomy"
+]
+packages = [
+    { include = "shade_ms" },
+]
+
+[tool.poetry.scripts]
+shadems = {reference = "bin/shadems", type = "file"}
+
+[tool.poetry.dependencies]
+python = "^3.8"
+datashader = "^0.13.0"
+dask-ms = { version = "^0.2.15", extras = ["xarray"] }
+holoviews = "^1.14.9"
+matplotlib = { version = "^3.6.0" }
+cmasher = "^1.6.3"
+future-fstrings = "^1.2.0"
+requests = "^2.27.1"
+numpy = "1.23.5" # Datashader installs the latest numpy which is in conflict with <=1.35.5 required by numba 
+dask = { extras = ["array"], version = "2022.9.1" } # Datashader installs the latest dask which is in conflict with <2023.0.0 required by dask-ms[array]
+pytest = { version = "^7.2.2", optional=true }
+pytest-flake8 = { version = "^1.1.1", optional=true }
+
+[tool.poetry.extras]
+testing = ["pytest", "pytest-flake8"]
+
+[build-system]
+requires = ["setuptools", "poetry-core"]
+build-backend = "poetry.core.masonry.api"

shade_ms/data_plots.py

@@ -165,7 +165,7 @@ def get_plot_data(msinfo, group_cols, mytaql, chan_freqs,
                           freqs=freqs,
                           wavel=wavel,
                           rows=group.row,
-                          baselines=baselines if baselines else np.array([baseline]))
+                          baselines=baselines if [baselines] else np.array([baseline]))
 
             nchan = len(group.chan)
             if flag is not None:

shade_ms/ms_info.py

@@ -1,11 +1,46 @@
-from MSUtils.msutils import STOKES_TYPES
 from casacore.tables import table
 import re
 import daskms
 import math
 import numpy as np
 from collections import OrderedDict
 
+STOKES_TYPES = {
+    0  : "Undefined",
+    1  : "I",
+    2  : "Q",
+    3  : "U",
+    4  : "V",
+    5  : "RR",
+    6  : "RL",
+    7  : "LR",
+    8  : "LL",
+    9  : "XX",
+    10 : "XY",
+    11 : "YX",
+    12 : "YY",
+    13 : "RX",
+    14 : "RY",
+    15 : "LX",
+    16 : "LY",
+    17 : "XR",
+    18 : "XL",
+    19 : "YR",
+    20 : "YL",
+    21 : "PP",
+    22 : "PQ",
+    23 : "QP",
+    24 : "QQ",
+    25 : "RCircular",
+    26 : "LCircular",
+    27 : "Linear",
+    28 : "Ptotal",
+    29 : "Plinear",
+    30 : "PFtotal",
+    31 : "PFlinear",
+    32 : "Pangle",
+}
+
 class NamedList(object):
     """Holds a list of names (e.g. field names), and provides common indexing and subset operations"""