Merge c73ce7a into d1de71f

.github/workflows/python-package.yml → .github/workflows/ci-tests.yml

@@ -32,7 +32,7 @@ jobs:
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest pytest-cov coveralls
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        if [ -f test_requirements.txt ]; then pip install -r test_requirements.txt; fi
+        if [ -f requirements_tests.txt ]; then pip install -r requirements_tests.txt; fi
         pip install -e .
     
     # - name: Lint with flake8
@@ -51,3 +51,6 @@ jobs:
       with:
         github-token: ${{ secrets.GITHUB_TOKEN }}
         path-to-lcov: coverage.lcov
+
+    - name: Open Journals PDF Generator
+      uses: openjournals/openjournals-draft-action@v.1.0

.github/workflows/draft-pdf.yml

@@ -0,0 +1,24 @@
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: joss/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: joss/paper.pdf
+

.gitignore

@@ -136,4 +136,5 @@ dmypy.json
 *.sublime-project
 *.sublime-workspace
 
-mytests
+mytests
+docs_deposit

CHANGELOG.md

@@ -1,51 +1,82 @@
 # CHANGELOG
 
-- 31/05/22
-    - Major changes, that affect the template structure:
-        - new field: 'lensing_entity'
-            - a list of either 'galaxy'-type objects or 'external_shear'-type objects
-            - each have a redshift, a name, etc... but 'external_shear' items can not have light profiles
-        - 'light_model' and 'mass_model' are now themselves list of profiles: there is no sub-field 'profiles' anymore
-        - 'lens_object' and 'lens_sample' have been removed. It means that ONE coolest template is related ONE lens system
-        - 'cosmology' is now outside of 'lens_model'
+## 04/10/22
+
+- The `ExternalShear` object has been replaced ba a more general `MassField` object. This is for supporting higher-order lensing fields such as flexion in the future. The two supported types of `LensingEntity` are thus `Galaxy` and `MassField`.
+
+- The type of lensing entity now reflects their class name. For instance, before it was `'galaxy'`, now it is `'Galaxy'`.
+
+- The single parameter of the `GaussianPSF` has changed from the standard deviation `std_dev` to the more widely used full width at half maximum `fwhm`.
+
+
+## 14/10/22
+
+### Major changes:
+
+- the path to submodules changed: `coolest.template.api` is now `coolest.template.classes`. This is because the API will now be formally containing analysis tools (in the future coolest.api submodule)
+- a single PixelatedRegularGrid class is now used for the observation image data, pixelated PSF, and pixelated light and mass profiles
+
+### Minor changes:
+
+- reorganized the repository structure, `coolest` is now at the root
+- the example of template generation is now in the `examples` directory
+- a 'DOC' mode has been added to the root COOLEST class (for usage with the documentation website, see separate repository)
+
+
+## 02/06/22
+
+### Major changes
+
+These affect the template structure:
+
+- hierachy levels 'lens_sample', 'lens_object' and 'lens_model' jave been removed; 'lensing_entities' is the relevant field now for model choices.
+- the 'origin' is at the root level
+
+### Standard changes:
+
+- the PSF can now be either a GaussianPSF, or a PixelatedPSF
+- the noise can now be one of the following choices: UniformGaussianNoise, NoiseMap, NoiseRealization, InstrumentalNoise, DrizzledNoise
+- the FitsFile object is now more explicit, renamed PixelFitsFile and containing number of pixels and pixel size
+
+### Minor changes:
+
+- renaming of classes
+- COOLEST standard now supports two distinct modes: 'MAP' to store model results, and 'MOCK' for simulating an observation
+
+
+##  31/05/22
+
+### Major changes
+Theese affect the template structure:
+
+- new field: 'lensing_entity'
+
+    - a list of either 'galaxy'-type objects or 'external_shear'-type objects
+    - each have a redshift, a name, etc... but 'external_shear' items can not have light profiles
 
-    - Standard changes:
-        - new field: 'instrument' 
-            - with optional 'image' fits file; if not provided, the 'mode' should be 'mock' (automatic via the API)
-            - with 'noise' sub-fields, optionally with a 'noise_map', option for including Poisson noise or not
-        - new field: 'observation'
-            - with 'psf' sub-fields, as a fits file for the psf kernel and potentially different pixel size
+- 'light_model' and 'mass_model' are now themselves list of profiles: there is no sub-field 'profiles' anymore
+- 'lens_object' and 'lens_sample' have been removed. It means that ONE coolest template is related ONE lens system
+- 'cosmology' is now outside of 'lens_model'
+
+### Standard changes
+
+- new field: 'instrument'
+
+    - with optional 'image' fits file; if not provided, the 'mode' should be 'mock' (automatic via the API)
+    - with 'noise' sub-fields, optionally with a 'noise_map', option for including Poisson noise or not
+
+- new field: 'observation'
+
+    - with 'psf' sub-fields, as a fits file for the psf kernel and potentially different pixel size
 
-    - Minor changes:
-        - new field: 'meta'
-            - for more flexbility for storing metadata, e.g. the name and version of the modeling code used to update/read the file
-            - for now it contains one sub-field: the 'mode' is set 'mock' if the coolest file is used for mocking, or 'model' if used to store modeling results
-        - new field: 'standard'
-            - defines more explicitely the standard system: 'coolest'
-        - many descriptive fields have been removed by default, as set in the CoolestStandard module (python class attributes were not removed though)
-
-
-- 02/06/22
-    - Major changes, that affect the template structure:
-        - hierachy levels 'lens_sample', 'lens_object' and 'lens_model' jave been removed; 'lensing_entities' is the relevant field now for model choices.
-        - the 'origin' is at the root level
-
-    - Standard changes:
-        - the PSF can now be either a GaussianPSF, or a PixelatedPSF
-        - the noise can now be one of the following choices: UniformGaussianNoise, NoiseMap, NoiseRealization, InstrumentalNoise, DrizzledNoise
-        - the FitsFile object is now more explicit, renamed PixelFitsFile and containing number of pixels and pixel size
-
-    - Minor changes:
-        - renaming of classes
-        - COOLEST standard now supports two distinct modes: 'MAP' to store model results, and 'MOCK' for simulating an observation
-
-
-- 14/10/22
-    - Major changes:
-        - the path to submodules changed: `coolest.template.api` is now `coolest.template.classes`. This is because the API will now be formally containing analysis tools (in the future coolest.api submodule)
-        - a single PixelatedRegularGrid class is now used for the observation image data, pixelated PSF, and pixelated light and mass profiles
-
-    - Minor changes:
-        - reorganized the repository structure, `coolest` is now at the root
-        - the example of template generation is now in the `examples` directory
-        - a 'DOC' mode has been added to the root COOLEST class (for usage with the documentation website, see separate repository)
+### Minor changes:
+
+- new field: 'meta'
+
+    - for more flexbility for storing metadata, e.g. the name and version of the modeling code used to update/read the file
+    - for now it contains one sub-field: the 'mode' is set 'mock' if the coolest file is used for mocking, or 'model' if used to store modeling results
+
+- new field: 'standard'
+    - defines more explicitely the standard system: 'coolest'
+
+- many descriptive fields have been removed by default, as set in the CoolestStandard module (python class attributes were not removed though)

Makefile

@@ -0,0 +1,9 @@
+PKG_VERSION = $(shell python setup.py --version)
+
+build-docs:
+	# pip install -r requirements_docs.txt
+	sphinx-build -b html docs docs/_build/html
+
+
+clean-docs:
+	rm -r docs/_build

README.md

@@ -2,6 +2,7 @@
 
 ![License](https://img.shields.io/github/license/aymgal/COOLEST)
 ![PyPi python support](https://img.shields.io/badge/Python-3.7-blue)
+[![Documentation Status](https://readthedocs.org/projects/coolest/badge/?version=latest)](https://coolest.readthedocs.io/en/latest/?badge=latest)
 [![Tests](https://github.com/aymgal/COOLEST/actions/workflows/python-package.yml/badge.svg?branch=main)](https://github.com/aymgal/COOLEST/actions/workflows/python-package.yml)
 [![Coverage Status](https://coveralls.io/repos/github/aymgal/COOLEST/badge.svg)](https://coveralls.io/github/aymgal/COOLEST)
 

coolest/__init__.py

@@ -13,6 +13,7 @@
 __author__ = 'COOLEST developers'
 __email__ = 'aymeric.galan@gmail.com'
 __year__ = '2021'
+__credits__ = 'COOLEST developers'
 __url__ = 'https://github.com/aymgal/COOLEST'
 __description__ = 'Standard for Strong Gravitational Lens Modeling'
 __python__ = '>=3.7'
@@ -27,3 +28,4 @@
 __about__ = ('{} Author: {}, Email: {}, Year: {}, {}'
              ''.format(__name__, __author__, __email__, __year__,
                        __description__))
+