Merge pull request #45 from ratt-ru/chaos

Chaos

.github/workflows/publish_package.yml

@@ -1,31 +1,41 @@
-# This workflows will upload a Python Package using Twine when a release is created
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
 
 name: Upload Python Package
 
 on:
   release:
-    types: [created]
+    types: [published]
+
+permissions:
+  contents: read
 
 jobs:
   deploy:
 
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v1
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
       with:
         python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: __token__
-        TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+    - name: Install Poetry
+      uses: snok/install-poetry@v1
+      with:
+        version: 1.4.0
+        virtualenvs-create: true
+        installer-parallel: false
+    - name: Install package
       run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+        poetry install --with docs --no-interaction
+    - name: Build and publish to pypi
+      uses: JRubics/[email protected]
+      with:
+        pypi_token: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/test_installation.yml

@@ -23,51 +23,54 @@ jobs:
       uses: actions/setup-python@v1
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
+    - name: Install Poetry
+      uses: snok/install-poetry@v1
+      with:
+        version: 1.4.0
+        virtualenvs-create: true
+        installer-parallel: false
+    - name: Install package
       run: |
-        python -m pip install --upgrade pip
-        pip install --upgrade setuptools wheel
-        pip install flake8 pytest
-        pip install .
+          poetry install --with tests --no-interaction
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        poetry run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        poetry run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test conversion to .txt models
       run: |
-        tigger-convert $GITHUB_WORKSPACE/test/3C147-HI6.refmodel.lsm.html /tmp/output.txt -f \
+        poetry run tigger-convert $GITHUB_WORKSPACE/test/3C147-HI6.refmodel.lsm.html /tmp/output.txt -f \
           --output-format "name ra_d dec_d i q u v i q u v spi rm emaj_s emin_s pa_d freq0"
-        tigger-convert $GITHUB_WORKSPACE/test/3C147-HI6.refmodel.lsm.html /tmp/output.recentred.txt -f --center 85.5deg,49.9deg --rename \
+        poetry run tigger-convert $GITHUB_WORKSPACE/test/3C147-HI6.refmodel.lsm.html /tmp/output.recentred.txt -f --center 85.5deg,49.9deg --rename \
           --output-format "name ra_d dec_d i q u v i q u v spi rm emaj_s emin_s pa_d freq0"
         echo "Checking reference LSM"
         diff $GITHUB_WORKSPACE/test/3C147-HI6.refmodel.reference.txt /tmp/output.txt
         echo "Checking recentred reference LSM"
         diff $GITHUB_WORKSPACE/test/3C147-HI6.refmodel.recentred.reference.txt /tmp/output.recentred.txt
     - name: Test reverse conversion to .lsm.html models
       run: |
-        tigger-convert /tmp/output.txt /tmp/output.lsm.html -f
+        poetry run tigger-convert /tmp/output.txt /tmp/output.lsm.html -f
     - name: Test .gaul conversions
       run: |
-        tigger-convert $GITHUB_WORKSPACE/test/deep4.gaul /tmp/deep4.lsm.html -f 
-        tigger-convert $GITHUB_WORKSPACE/test/deep4.gaul /tmp/deep4.txt -f --output-format "name ra_d dec_d i q u v spi rm emaj_s emin_s pa_d freq0"
+        poetry run tigger-convert $GITHUB_WORKSPACE/test/deep4.gaul /tmp/deep4.lsm.html -f 
+        poetry run tigger-convert $GITHUB_WORKSPACE/test/deep4.gaul /tmp/deep4.txt -f --output-format "name ra_d dec_d i q u v spi rm emaj_s emin_s pa_d freq0"
         diff $GITHUB_WORKSPACE/test/deep4.reference.txt /tmp/deep4.txt
     - name: Test .AIPSCC conversions
       run: |
         gunzip <$GITHUB_WORKSPACE/test/3C147-L-A-CLEAN.fits.gz >/tmp/3C147-L-A-CLEAN.fits
-        tigger-convert /tmp/3C147-L-A-CLEAN.fits /tmp/3C147-L-A-CLEAN.fits.lsm.html -f
-        tigger-convert /tmp/3C147-L-A-CLEAN.fits.lsm.html /tmp/3C147-L-A-CLEAN.txt -f --output-format "name ra_d dec_d i q u v"
+        poetry run tigger-convert /tmp/3C147-L-A-CLEAN.fits /tmp/3C147-L-A-CLEAN.fits.lsm.html -f
+        poetry run tigger-convert /tmp/3C147-L-A-CLEAN.fits.lsm.html /tmp/3C147-L-A-CLEAN.txt -f --output-format "name ra_d dec_d i q u v"
         zdiff $GITHUB_WORKSPACE/test/3C147-L-A-CLEAN.txt.gz /tmp/3C147-L-A-CLEAN.txt
     - name: Testing tigger-restore and tigger-make-brick
       run: |
         cp $GITHUB_WORKSPACE/test/3C147tmp.fits /tmp
-        tigger-make-brick $GITHUB_WORKSPACE/test/3C147-HI6.refmodel.lsm.html /tmp/3C147tmp.fits 
-        tigger-restore -f $GITHUB_WORKSPACE/test/3C147tmp.fits $GITHUB_WORKSPACE/test/3C147-HI6.refmodel.lsm.html /tmp/restored.fits
+        poetry run tigger-make-brick $GITHUB_WORKSPACE/test/3C147-HI6.refmodel.lsm.html /tmp/3C147tmp.fits 
+        poetry run tigger-restore -f $GITHUB_WORKSPACE/test/3C147tmp.fits $GITHUB_WORKSPACE/test/3C147-HI6.refmodel.lsm.html /tmp/restored.fits
     - name: Test tigger-tag
       run: |
-        tigger-tag $GITHUB_WORKSPACE/test/3C147-HI6.refmodel.lsm.html 'r<0.5d' inner=1 -o /tmp/tmp.lsm.html -f
+        poetry run tigger-tag $GITHUB_WORKSPACE/test/3C147-HI6.refmodel.lsm.html 'r<0.5d' inner=1 -o /tmp/tmp.lsm.html -f
     - name: Test .lsm to ds9 region file conversion
       run: |
         echo "Checking lsm.html to .reg conversion"
-        tigger-convert $GITHUB_WORKSPACE/test/3C147-HI6.refmodel.lsm.html /tmp/3C147-HI6.refmodel.lsm.reg -f 
+        poetry run tigger-convert $GITHUB_WORKSPACE/test/3C147-HI6.refmodel.lsm.html /tmp/3C147-HI6.refmodel.lsm.reg -f 

.travis/py3.docker

@@ -1,100 +1,38 @@
-FROM kernsuite/base:6
+FROM kernsuite/base:9
 
 RUN docker-apt-install python3-casacore casacore-dev casacore-data makems casarest \
                        python3-pip git wget cmake libblitz0-dev libqdbm-dev \
                        libfftw3-dev wcslib-dev libcfitsio-dev \
-                       'libcasa-*' liblapack-dev libatlas-base-dev
+                       'libcasa-*' liblapack-dev libatlas-base-dev 2to3
 
-RUN pip3 install -U pip setuptools wheel
+RUN pip install -U pip setuptools wheel
 #######################################
 # Install python 3 meqtrees
 #######################################
 
-WORKDIR /code
-ADD . /code/tigger-lsm
-RUN pip3 install ./tigger-lsm
 
 # add additional Timba dependencies
-RUN docker-apt-install python3-pyqt4 python3-pyqt5
+RUN docker-apt-install meqtrees-timba
 WORKDIR /src
-RUN wget https://codeload.github.com/ska-sa/meqtrees-cattery/tar.gz/refs/tags/v1.7.1 && \
-    tar zxvf v1.7.1 && \
-    rm v1.7.1 
-RUN wget https://codeload.github.com/ska-sa/purr/tar.gz/refs/tags/v1.5.0 && \
-    tar zxvf v1.5.0 && \
-    rm v1.5.0
-RUN wget https://codeload.github.com/ska-sa/owlcat/tar.gz/refs/tags/v1.6.0 && \
-    tar zxvf v1.6.0 && \
-    rm v1.6.0
-RUN wget https://codeload.github.com/ska-sa/kittens/tar.gz/refs/tags/v1.4.3 && \
-    tar zxvf v1.4.3 && \
-    rm v1.4.3
 RUN wget https://codeload.github.com/ska-sa/pyxis/tar.gz/refs/tags/v1.7.1 && \
     tar zxvf v1.7.1 && \
     rm v1.7.1
 
-RUN pip3 install ./meqtrees-cattery-1.7.1 ./purr-1.5.0 ./owlcat-1.6.0 ./kittens-1.4.3
-RUN pip3 install -e ./pyxis-1.7.1
-
-WORKDIR /src
-RUN wget https://codeload.github.com/ska-sa/meqtrees-timba/tar.gz/refs/tags/v1.8.0 && \
-    tar zxvf v1.8.0 && \
-    rm v1.8.0
-RUN mkdir /src/meqtrees-timba-1.8.0/build
-WORKDIR /src/meqtrees-timba-1.8.0/build
-RUN cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release -DENABLE_PYTHON_3=ON ..
-RUN make
-RUN make install
-RUN ldconfig
+WORKDIR /code
+ADD . /code/tigger-lsm
+RUN pip install ./tigger-lsm
 
-RUN update-alternatives --install /usr/bin/python python /usr/bin/python3.6 2
 # basic install tests
+RUN pip install pynose owlcat
 RUN flag-ms.py --help
 RUN meqtree-pipeliner.py --help
 RUN pyxis --help
 
-#######################################
-# run oleg's new tests
-#######################################
-ENV GITHUB_WORKSPACE=/code/tigger-lsm
-# Test conversion to .txt models
-RUN tigger-convert $GITHUB_WORKSPACE/test/3C147-HI6.refmodel.lsm.html /tmp/output.txt -f \
-    --output-format "name ra_d dec_d i q u v i q u v spi rm emaj_s emin_s pa_d freq0"
-RUN tigger-convert $GITHUB_WORKSPACE/test/3C147-HI6.refmodel.lsm.html /tmp/output.recentred.txt -f --center 85.5deg,49.9deg --rename \
-    --output-format "name ra_d dec_d i q u v i q u v spi rm emaj_s emin_s pa_d freq0"
-RUN echo "Checking reference LSM"
-RUN diff $GITHUB_WORKSPACE/test/3C147-HI6.refmodel.reference.txt /tmp/output.txt
-RUN echo "Checking recentred reference LSM"
-RUN diff $GITHUB_WORKSPACE/test/3C147-HI6.refmodel.recentred.reference.txt /tmp/output.recentred.txt
-
-#Test reverse conversion to .lsm.html models
-RUN tigger-convert /tmp/output.txt /tmp/output.lsm.html -f
-
-#Test .gaul conversions
-RUN tigger-convert $GITHUB_WORKSPACE/test/deep4.gaul /tmp/deep4.lsm.html -f 
-RUN tigger-convert $GITHUB_WORKSPACE/test/deep4.gaul /tmp/deep4.txt -f --output-format "name ra_d dec_d i q u v spi rm emaj_s emin_s pa_d freq0"
-RUN diff $GITHUB_WORKSPACE/test/deep4.reference.txt /tmp/deep4.txt
-
-# Test .AIPSCC conversions
-RUN gunzip <$GITHUB_WORKSPACE/test/3C147-L-A-CLEAN.fits.gz >/tmp/3C147-L-A-CLEAN.fits
-RUN tigger-convert /tmp/3C147-L-A-CLEAN.fits /tmp/3C147-L-A-CLEAN.fits.lsm.html -f
-RUN tigger-convert /tmp/3C147-L-A-CLEAN.fits.lsm.html /tmp/3C147-L-A-CLEAN.txt -f --output-format "name ra_d dec_d i q u v"
-RUN zdiff $GITHUB_WORKSPACE/test/3C147-L-A-CLEAN.txt.gz /tmp/3C147-L-A-CLEAN.txt
-
-# Testing tigger-restore and tigger-make-brick
-RUN cp $GITHUB_WORKSPACE/test/3C147tmp.fits /tmp
-RUN tigger-make-brick $GITHUB_WORKSPACE/test/3C147-HI6.refmodel.lsm.html /tmp/3C147tmp.fits 
-RUN tigger-restore -f $GITHUB_WORKSPACE/test/3C147tmp.fits $GITHUB_WORKSPACE/test/3C147-HI6.refmodel.lsm.html /tmp/restored.fits
-
-#Test tigger-tag
-RUN tigger-tag $GITHUB_WORKSPACE/test/3C147-HI6.refmodel.lsm.html 'r<0.5d' inner=1 -o /tmp/tmp.lsm.html -f
-
 #######################################
 # end to end test
 #######################################
-RUN pip3 install nose
 WORKDIR /src/pyxis-1.7.1/Pyxis/recipes/meqtrees-batch-test
-RUN python3 -m "nose"
+RUN pynose
 
 ENTRYPOINT ["meqtree-pipeliner.py"]
 CMD ["--help"]

Tigger/bin/tigger-convert → Tigger/bin/tigger_convert.py

@@ -34,6 +34,7 @@
 
 import numpy
 import os.path
+import Cattery.Siamese.OMS.Utils as Utils
 
 DEG = math.pi / 180
 
@@ -81,7 +82,7 @@ def rotatelm(l0, m0, rotangle):
     return l, m
 
 
-if __name__ == '__main__':
+def main():
     import Kittens.utils
 
     _verbosity = Kittens.utils.verbosity(name="convert-model")
@@ -460,7 +461,7 @@ def convert_coordinates(coords):
                 # recompute 'r' attribute (unless --center is in effect, in which case it's going to be done anyway below)
                 if options.refresh_r:
                     for src in model2.sources:
-                        src.setAttribute('r', Coordinates.angular_dist_pos_angle(ra0, dec0, *model.fieldCenter())[0])
+                        src.setAttribute('r', Coordinates.angular_dist_pos_angle(src.pos.ra, src.pos.dec, *model.fieldCenter())[0])
             print("Appended %d sources from %s (%s)" % (len(model2.sources), filename, append_doc))
 
     # apply center, if specified
@@ -514,8 +515,8 @@ def convert_coordinates(coords):
                 tags = ff[3:] if len(ff) > 3 else []
             except:
                 parser.error("Invalid --add-brick setting %s" % brickspec)
-            if [src.name for src in sources if src.name == name]:
-                print("Error: model already contains a source named '%s'" % name)
+            if [src.name for src in sources if src.name == srcname]:
+                print("Error: model already contains a source named '%s'" % srcname)
             # add brick
             from astropy.io import fits as pyfits
             from astLib.astWCS import WCS
@@ -660,12 +661,6 @@ def getTagValue(src, tag):
             REIM = "re", "im"
             REALIMAG = dict(re="real", im="imag")
 
-            # get the Cattery
-            for varname in 'CATTERY_PATH', "MEQTREES_CATTERY_PATH":
-                if varname in os.environ:
-                    sys.path.append(os.environ[varname])
-
-            import Siamese.OMS.Utils as Utils
 
 
             def make_beam_filename(filename_pattern, corr, reim):
@@ -681,7 +676,7 @@ def make_beam_filename(filename_pattern, corr, reim):
             filename_real = []
             filename_imag = []
             # load beam interpolator
-            import Siamese.OMS.InterpolatedBeams as InterpolatedBeams
+            import Cattery.Siamese.OMS.InterpolatedBeams as InterpolatedBeams
 
             vbs = []
             for icorr, corr in enumerate(CORRS_XY if options.linear_pol else CORRS_RL):

Tigger/bin/tigger-make-brick → Tigger/bin/tigger_make_brick.py

@@ -41,7 +41,7 @@
 
 NATIVE = "Tigger"
 
-if __name__ == '__main__':
+def main():
     import Kittens.utils
 
     _verbosity = Kittens.utils.verbosity(name="convert-model")
@@ -221,7 +221,7 @@
                 src.flux.I = max_flux
                 src.shape.ex, src.shape.ey = sx, sy
                 src.shape.nx, src.shape.ny = nx, ny
-                src.shape.pad = pad
+                src.shape.pad = options.pad
                 break
         # not contained, make new source object
         else:

Tigger/bin/tigger-restore → Tigger/bin/tigger_restore.py

@@ -32,7 +32,7 @@
 from astropy.io import fits as pyfits
 from past.builtins import cmp
 
-if __name__ == '__main__':
+def main():
 
     import Tigger.Models.Formats
     from Tigger.Models.Formats import ASCII
@@ -196,7 +196,7 @@
             if not isinstance(dum, float):
                 raise TypeError("Primary beam expression does not evaluate to a float")
         except Exception as exc:
-            print("Bad primary beam expression '%s': %s" % (pb, str(exc)))
+            print("Bad primary beam expression '%s': %s" % (options.pb, str(exc)))
             sys.exit(1)
         if not freq:
             print("Model must contain a reference requency, or else specify one with --freq.")

Tigger/bin/tigger-tag → Tigger/bin/tigger_tag.py

@@ -65,7 +65,7 @@ def transfer_tags(fromlsm, lsm, output, tags, tolerance, tigger):
     model.save(output)
 
 
-if __name__ == '__main__':
+def main():
     import Kittens.utils
 
     _verbosity = Kittens.utils.verbosity(name="convert-model")
@@ -172,13 +172,15 @@ def transfer_tags(fromlsm, lsm, output, tags, tolerance, tigger):
 
     # This is where we accumulate the result of selection arguments, until we hit the first tagging argument.
     # Initially None, meaning no explicit selection
+    global selected_ids
     selected_ids = None
 
     # This is where we put the selection when we hit the first tagging argument.
+    global selection
     selection = None
 
     # this is set to true when the selection is listed
-    listed = False
+    global listed
     # set to true when the model is modified
     modified = False
 
@@ -300,7 +302,7 @@ def lookupObject(src, tagname):
             # else some other type is specified -- use it to convert the value
             elif typename:
                 try:
-                    newval = getattr(__builtin__, typename)(value)
+                    newval = getattr(globals()["__builtin__"], typename)(value)
                 except:
                     print("Can't parse \"%s\" as a value of type %s" % (value, typename))
                     sys.exit(2)