Merge pull request #36 from ratt-ru/write_regions_catalogs

Write regions and catalogs

.github/workflows/test_installation.yml → .github/workflows/python-package.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v2
@@ -64,4 +64,4 @@ jobs:
   
     - name: Test command
       run: |
-        poetry run breizorro -h
+        poetry run breizorro --help

MANIFEST.in

@@ -1,3 +1,4 @@
 include LICENSE
 include README.rst
 include requirements.txt
+include breizorro/breizorro.yaml

README.rst

@@ -30,63 +30,11 @@ To show help message and exit
    
    $ breizorro --help
 
-     breizorro.breizorro - 2022-08-24 11:07:39,311 INFO - Welcome to breizorro
-     breizorro.breizorro - 2022-08-24 11:07:39,375 INFO - Version: 0.1.1
-     breizorro.breizorro - 2022-08-24 11:07:39,375 INFO - Usage: breizorro --help
-     usage: breizorro [-h] [-r IMAGE] [-m MASK] [-t THRESHOLD] [-b BOXSIZE]
-                      [--savenoise] [--merge MASKs|REGs) [MASK(s|REGs) ...]]
-                      [--subtract MASK(s|REGs) [MASK(s|REGs ...]]
-                      [--number-islands] [--remove-islands N|COORD [N|COORD ...]]
-                      [--ignore-missing-islands]
-                      [--extract-islands N|COORD [N|COORD ...]]
-                      [--minimum-size MINSIZE] [--make-binary] [--invert]
-                      [--dilate R] [--erode N] [--fill-holes] [--sum-peak SUM_PEAK]
-                      [-o OUTFILE] [--gui]
-
-     breizorro [options] --restored-image restored_image
-
-     optional arguments:
-          -h, --help            show this help message and exit
-          -r IMAGE, --restored-image IMAGE
-                                Restored image file from which to build mask
-          -m MASK, --mask-image MASK
-                                Input mask file(s). Either --restored-image or --mask-
-                                image must be specfied.
-          -t THRESHOLD, --threshold THRESHOLD
-                                Sigma threshold for masking (default = 6.5)
-          -b BOXSIZE, --boxsize BOXSIZE
-                                Box size over which to compute stats (default = 50)
-          --savenoise           Enable to export noise image as FITS file (default=do
-                                not save noise image)
-          --merge MASK(s)|REG(s) [MASK(s)|REG(s) ...]
-                                Merge in one or more masks or region files
-          --subtract MASK(s)|REG(s) [MASK(s)|REG(s) ...]
-                                Subract one or more masks or region files
-          --number-islands      Number the islands detected (default=do not number
-                                islands)
-          --remove-islands N|COORD [N|COORD ...]
-                                List of islands to remove from input mask. e.g.
-                                --remove-islands 1 18 20 20h10m13s,14d15m20s
-          --ignore-missing-islands
-                                If an island specified by coordinates does not exist,
-                                do not throw an error
-          --extract-islands N|COORD [N|COORD ...]
-                                List of islands to extract from input mask. e.g.
-                                --extract-islands 1 18 20 20h10m13s,14d15m20s
-          --minimum-size MINSIZE
-                                Remove islands that have areas fewer than or equal to
-                                the specified number of pixels
-          --make-binary         Replace all island numbers with 1
-          --invert              Invert the mask
-          --dilate R            Apply dilation with a radius of R pixels
-          --erode N             Apply N iterations of erosion
-          --fill-holes          Fill holes (i.e. entirely closed regions) in mask
-          --sum-peak SUM_PEAK   Sum to peak ratio of flux islands to mask in original
-                                image.e.g. --sum-peak 100 will mask everything with a
-                                ratio above 100
-          -o OUTFILE, --outfile OUTFILE
-                                Suffix for mask image (default based on input name
-          --gui                 Open mask in gui.
+=============
+Documentation
+=============
+
+Documentation is available on the GitHub page_.
 
 =======
 License
@@ -116,3 +64,4 @@ standards pep8_.
 .. _source: https://github.com/ratt-ru/breizorro
 .. _license: https://github.com/ratt-ru/breizorro/blob/main/LICENSE
 .. _pep8: https://www.python.org/dev/peps/pep-0008
+.. _page: https://ratt-ru.github.io/breizorro

_config.yml

@@ -0,0 +1,5 @@
+title: Breizorro
+description: Image masking and cataloguing suite
+show_downloads: true
+google_analytics: 
+theme: jekyll-theme-midnight