Merge pull request #1 from Mulan-94/sade

Moving from smops to Sade

.github/ISSUE_TEMPLATE.md

@@ -1,4 +1,4 @@
-* smops version:
+* sade version:
 * Python version:
 * Operating System:
 

.github/workflows/test.yml

@@ -20,8 +20,8 @@ jobs:
           python-vresion: ${{ matrix.python-version }}
       - name: Display Python version
         run: python -c "import sys; print(sys.version)"
-      - name: Install smops
+      - name: Install sade
         run: |
           python -m pip install --upgrade pip
           pip install .
-          smops -v
+          sade -v

CONTRIBUTING.rst

@@ -15,7 +15,7 @@ Types of Contributions
 Report Bugs
 ~~~~~~~~~~~
 
-Report bugs at https://github.com/mulan-94/smops/issues.
+Report bugs at https://github.com/mulan-94/sade/issues.
 
 If you are reporting a bug, please include:
 
@@ -38,14 +38,14 @@ and "help wanted" is open to whoever wants to implement it.
 Write Documentation
 ~~~~~~~~~~~~~~~~~~~
 
-smops could always use more documentation, whether as part of the
-official smops docs, in docstrings, or even on the web in blog posts,
+sade could always use more documentation, whether as part of the
+official sade docs, in docstrings, or even on the web in blog posts,
 articles, and such.
 
 Submit Feedback
 ~~~~~~~~~~~~~~~
 
-The best way to send feedback is to file an issue at https://github.com/mulan-94/smops/issues.
+The best way to send feedback is to file an issue at https://github.com/mulan-94/sade/issues.
 
 If you are proposing a feature:
 
@@ -57,17 +57,17 @@ If you are proposing a feature:
 Get Started!
 ------------
 
-Ready to contribute? Here's how to set up `smops` for local development.
+Ready to contribute? Here's how to set up `sade` for local development.
 
-1. Fork the `smops` repo on GitHub.
+1. Fork the `sade` repo on GitHub.
 2. Clone your fork locally::
 
-    $ git clone [email protected]:your_name_here/smops.git
+    $ git clone [email protected]:your_name_here/sade.git
 
 3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
 
-    $ mkvirtualenv smops
-    $ cd smops/
+    $ mkvirtualenv sade
+    $ cd sade/
     $ python setup.py develop
 
 4. Create a branch for local development::
@@ -79,7 +79,7 @@ Ready to contribute? Here's how to set up `smops` for local development.
 5. When you're done making changes, check that your changes pass flake8 and the
    tests, including testing other Python versions with tox::
 
-    $ flake8 smops tests
+    $ flake8 sade tests
     $ python setup.py test or pytest
     $ tox
 
@@ -103,15 +103,15 @@ Before you submit a pull request, check that it meets these guidelines:
    your new functionality into a function with a docstring, and add the
    feature to the list in README.rst.
 3. The pull request should work for Python 3.5, 3.6, 3.7 and 3.8, and for PyPy. Check
-   https://travis-ci.com/mulan-94/smops/pull_requests
+   https://travis-ci.com/mulan-94/sade/pull_requests
    and make sure that the tests pass for all supported Python versions.
 
 Tips
 ----
 
 To run a subset of tests::
 
-$ pytest tests.test_smops
+$ pytest tests.test_sade
 
 
 Deploying

HISTORY.rst

@@ -2,7 +2,13 @@
 History
 =======
 
-0.1.0 (2022-09-12)
+0.1.2 (2022-09-14)
 ------------------
+* Change name from smops to sade
+* Added `output-prefix` argument
+* Removed `output-dir` argument
+
 
+0.1.0 (2022-09-12)
+------------------
 * First release on PyPI.

Makefile

@@ -48,7 +48,7 @@ clean-test: ## remove test and coverage artifacts
 	rm -fr .pytest_cache
 
 lint/flake8: ## check style with flake8
-	flake8 smops tests
+	flake8 sade tests
 
 lint: lint/flake8 ## check style
 
@@ -59,15 +59,15 @@ test-all: ## run tests on every Python version with tox
 	tox
 
 coverage: ## check code coverage quickly with the default Python
-	coverage run --source smops -m pytest
+	coverage run --source sade -m pytest
 	coverage report -m
 	coverage html
 	$(BROWSER) htmlcov/index.html
 
 docs: ## generate Sphinx HTML documentation, including API docs
-	rm -f docs/smops.rst
+	rm -f docs/sade.rst
 	rm -f docs/modules.rst
-	sphinx-apidoc -o docs/ smops
+	sphinx-apidoc -o docs/ sade
 	$(MAKE) -C docs clean
 	$(MAKE) -C docs html
 	$(BROWSER) docs/_build/html/index.html

README.rst

@@ -1,37 +1,39 @@
 =====
-smops
+sade
 =====
 
 
-.. image:: https://img.shields.io/pypi/v/smops.svg
-        :target: https://pypi.python.org/pypi/smops
+.. image:: https://img.shields.io/pypi/v/sade.svg
+        :target: https://pypi.python.org/pypi/sade
 
 
-smops - (aka Smooth Operator) is a python package for interpolating channelised FITS model images over larger user-specified frequency channesl. i.e if you give smops 4 channel model fits images, it will return 16 model images. For example:
+sade (aka Smooth Operator) is a python package for interpolating channelised FITS model images onto user-specified higher resolution frequency grid. For example, you can give sade a set of 4 per-subband model FITS images, and ask it to return 16 model images, which can then be fed back into e.g. wsclean_ for a predict operation. Usage:
 
 .. code-block:: bash
 
-        smops --ms /ms/used/togen/images.ms -ip prefix-used-for-those-images -co 16 -order 4
+        sade --ms /ms/used/togen/images.ms -ip prefix-used-for-those-images -co 16 -order 4
 
 
 Its options are:
 
 .. code-block:: python
 
-        usage: smops [-h] [-od] [-nthreads] [-stokes] [-mem] --ms  -ip  -co  [-order]
+        usage: sade [-h] [-v] [-op] [-j] [-s] [-mem] -ms  -ip  -co  [-order]
 
         Refine model images in frequency
 
         optional arguments:
         -h, --help            show this help message and exit
-        -od , --output-dir    Where to put the output files.
-        -nthreads             Number of threads to use while writing out images
-        -stokes               Which stokes model to extrapolate. Write as single string e.g IQUV. Required when there are multiple Stokes
+        -v, --version         show program's version number and exit
+        -op , --output-prefix 
+                                What to prefix the new interpolated model name with.
+        -j , --num-threads    Number of threads to use while writing out output images
+        -s , --stokes         Which stokes model to extrapolate. Write as single string e.g IQUV. Required when there are multiple Stokes
                                 images in a directory. Default 'I'.
         -mem , --max-mem      Approximate memory cap in GB
 
         Required arguments:
-        --ms                  Input MS. Used for getting reference frequency
+        -ms , --ms            Input MS. Used for getting reference frequency
         -ip , --input-prefix 
                                 The input image prefix. The same as the one used for wsclean
         -co , --channels-out 
@@ -58,3 +60,4 @@ It was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ proj
 .. _`@o-smirnov`: https://github.com/o-smirnov
 .. _`@landmanbester`: https://github.com/landmanbester
 .. _`@ratt-ru`: https://github.com/ratt-ru
+.. _wsclean: https://gitlab.com/aroffringa/wsclean

smops/__init__.py → sade/__init__.py

@@ -1,5 +1,5 @@
-"""Top-level package for smops."""
+"""Top-level package for sade."""
 
 __author__ = AUTHOR = """L Andati"""
 __email__ = EMAIL = '[email protected]'
-__version__ = VERSION = '0.1.1'
+__version__ = VERSION = '0.1.2'

smops/smooth.py → sade/smooth.py

@@ -17,13 +17,13 @@
 
 
 from dask import compute
-from smops import VERSION
+from sade import VERSION
 
 
 GB = 2**30
 MAX_MEM = None
 
-def configure_logger(out_dir):
+def configure_logger(out_dir="."):
     formatter = logging.Formatter(
         datefmt='%H:%M:%S %d.%m.%Y',
         fmt="%(asctime)s : %(name)s - %(levelname)s - %(message)s")
@@ -32,7 +32,7 @@ def configure_logger(out_dir):
         os.makedirs(out_dir)
 
     l_handler = logging.FileHandler(
-        os.path.join(out_dir, "smooth-operator.log"), mode="w")
+        os.path.join(out_dir, "sade.log"), mode="w")
     l_handler.setLevel(logging.INFO)
     l_handler.setFormatter(formatter)
 
@@ -51,22 +51,24 @@ def configure_logger(out_dir):
 def get_arguments():
     parser = argparse.ArgumentParser(description="Refine model images in frequency")
     parser.add_argument("-v", "--version", action='version', version=f'%(prog)s {VERSION}')
-    parser.add_argument("-od", "--output-dir", dest="output_dir",
-        default="smooth-ops", metavar="",
-        help="Where to put the output files.")
-    parser.add_argument("-nthreads", dest="nthreads", default=10, metavar="",
-        type=int, help="Number of threads to use while writing out images")
-    parser.add_argument("-stokes", dest="stokes",
+    # parser.add_argument("-od", "--output-dir", dest="output_dir",
+    #     default="sade-output", metavar="",
+    #     help="Where to put the output files.")
+    parser.add_argument("-op", "--output-prefix", dest="output_pref",
+        default="sade-interp-model", metavar="",
+        help="What to prefix the new interpolated model name with.")
+    parser.add_argument("-j", "--num-threads", dest="nthreads", default=10, metavar="",
+        type=int, help="Number of threads to use while writing out output images")
+    parser.add_argument("-s", "--stokes", dest="stokes",
         default="I", metavar="", type=str,
         help="""Which stokes model to extrapolate. Write as single string e.g
         IQUV. Required when there are multiple Stokes images in a directory.
         Default 'I'.""")
     parser.add_argument("-mem", "--max-mem", dest="max_mem", default=None,
         type=int, metavar="",
-        help="Approximate memory cap in GB"
-        )
+        help="Approximate memory cap in GB")
     reqs = parser.add_argument_group("Required arguments")
-    reqs.add_argument("--ms", dest="ms_name", required=True, metavar="",
+    reqs.add_argument("-ms", "--ms", dest="ms_name", required=True, metavar="",
         help="Input MS. Used for getting reference frequency")
     reqs.add_argument("-ip", "--input-prefix", dest="input_prefix",
         required=True, metavar="",
@@ -304,7 +306,7 @@ def gen_fits_file_from_template(template_fits, center_freq, cdelt, new_data, out
     return
 
 
-def write_model_out(chan_num, chan_id, temp_fname, output_dir, cdelt, models, freqs):
+def write_model_out(chan_num, chan_id, temp_fname, out_pref, cdelt, models, freqs):
     """
     Write the new models output
 
@@ -319,8 +321,8 @@ def write_model_out(chan_num, chan_id, temp_fname, output_dir, cdelt, models, fr
         naming purposes.
     temp_fname: str
         Name of the template file that will be used
-    output_dir: str
-        Where the output will be dumped
+    out_pref: str
+        Prefix of the output models
     cdelt: float
         Channel width for this channel
     models: n-d array
@@ -332,9 +334,7 @@ def write_model_out(chan_num, chan_id, temp_fname, output_dir, cdelt, models, fr
     
     """
     # snitch.info(f"Channel number: {chan_num}, id: {chan_id}")
-    outname = os.path.basename(temp_fname)
-    outname = re.sub(r"-(\d){4}-", "-"+f"{chan_id}".zfill(4)+"-", outname)
-    outname = os.path.join(output_dir, outname)
+    outname = out_pref + '-' + f"{chan_id}".zfill(4) + "-model.fits"
     gen_fits_file_from_template(
         temp_fname, freqs[chan_id], cdelt,
         models[chan_num], outname)
@@ -344,9 +344,12 @@ def main():
     args = get_arguments().parse_args()
     global snitch, MAX_MEM
 
-    output_dir = args.output_dir
+    # output_dir = args.output_dir
+    # if not os.path.isdir(output_dir):
+    #     snitch.info(f"Creating output directory: {output_dir}")
+    #     os.makedirs(output_dir)
 
-    snitch = configure_logger(output_dir)
+    snitch = configure_logger()
 
     if args.max_mem is not None:
         MAX_MEM = args.max_mem
@@ -355,9 +358,7 @@ def main():
     snitch.info(f"Setting memory cap to: {MAX_MEM} GB")
 
 
-    if not os.path.isdir(output_dir):
-        snitch.info(f"Creating output directory: {output_dir}")
-        os.makedirs(output_dir)
+
 
     ref_freq = get_ms_ref_freq(args.ms_name)  
 
@@ -426,7 +427,7 @@ def main():
             with ThreadPoolExecutor(args.nthreads) as executor:
                 results = executor.map(
                     partial(write_model_out, temp_fname=images_list[0],
-                            output_dir=output_dir, cdelt=new_cdelt,
+                            out_pref=args.output_pref, cdelt=new_cdelt,
                             models=data, freqs=out_freqs), 
                     chan_range, chan_ids)
 

setup.cfg

@@ -1,13 +1,13 @@
 # https://setuptools.pypa.io/en/latest/userguide/declarative_config.html?
 # https://setuptools.pypa.io/en/latest/references/keywords.html
 [metadata]
-  name = smops
-  version = attr: smops.VERSION
+  name = sade
+  version = attr: sade.VERSION
   author = L. Andati
   email = [email protected]
   description = Python script for interpolating FITS model images over frequency
   long_description = file: README.rst, CHANGELOG.rst, LICENSE.rst
-  keywords = smops, model frequency interpolation, FITS images
+  keywords = sade, model frequency interpolation, FITS images
   license = MIT license
   license_files = file: LICENSE.rst
   url = https://github.com/mulan-94/smops

setup.py

@@ -8,8 +8,8 @@
 setup(
     entry_points={
         'console_scripts': [
-            'smops=smops.smooth:main',
+            'sade=sade.smooth:main',
         ],
     },
-    packages=find_packages(include=['smops', 'smops.*']),
+    packages=find_packages(include=['sade', 'sade.*']),
 )

tox.ini

@@ -10,7 +10,7 @@ python =
 [testenv:flake8]
 basepython = python
 deps = flake8
-commands = flake8 smops tests
+commands = flake8 sade tests
 
 [testenv]
 setenv =