v1.1 updates

.github/workflows/run_code_coverage.yml

@@ -0,0 +1,65 @@
+name: Run unit tests
+
+on: 
+  push:
+    branches:
+      - main
+      - dev
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.11"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools wheel
+      - name: Test with tox
+        run: |
+          pip install tox coverage
+          tox -e py
+      - name: Upload coverage data
+        uses: actions/upload-artifact@v3
+        with:
+          name: covdata
+          path: .coverage.*
+      - name: Download coverage data
+        uses: actions/download-artifact@v3
+        with:
+          name: covdata
+      - name: Combine
+        run: |
+          python -m coverage combine
+
+          # Report and write to summary.
+          python -m coverage report
+          python -m coverage report | sed 's/^/    /' >> $GITHUB_STEP_SUMMARY
+          python -m coverage json
+
+          export TOTAL=$(python -c "import json;print(json.load(open('coverage.json'))['totals']['percent_covered_display'])")
+          echo "total=$TOTAL" >> $GITHUB_ENV
+          echo "### Total coverage: ${TOTAL}%" >> $GITHUB_STEP_SUMMARY
+      - name: Make badge
+        uses: schneegans/[email protected]
+        with:
+          auth: ${{ secrets.GIST_TOKEN }}
+          gistID: de229c48256d967a1cb8b29dbf575602
+          filename: covbadge.json
+          label: code coverage
+          message: ${{ env.total }}%
+          minColorRange: 50
+          maxColorRange: 90
+          valColorRange: ${{ env.total }}

.github/workflows/run_unit_tests.yml

@@ -4,6 +4,7 @@ on:
   push:
     branches:
       - main
+      - dev
   pull_request:
     branches:
       - main
@@ -15,12 +16,12 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
@@ -36,5 +37,5 @@ jobs:
         continue-on-error: true
       - name: Test with tox
         run: |
-          pip install tox
-          tox -e py
+          pip install tox coverage
+          tox -e py

CITATION.cff

@@ -7,24 +7,37 @@ authors:
 - family-names: "Blackburn"
   given-names: "Lindy"
   orcid: "https://orcid.org/0000-0002-9030-642X"
-- family-names: "Hamilton"
-  given-names: "Linus"
+- family-names: "Chaves"
+  given-names: "Ryan"
+- family-names: "Doeleman"
+  given-names: "Sheperd S."
+- family-names: "Freeman"
+  given-names: "Mark"
+- family-names: "Issaoun"
+  given-names: "Sara"
+  orcid: "https://orcid.org/0000-0002-5297-921X"
 - family-names: "Johnson"
   given-names: "Michael D."
   orcid: "https://orcid.org/0000-0002-4120-3029"
 - family-names: "Lindahl"
   given-names: "Greg"
   orcid: "https://orcid.org/0000-0002-6100-4772"
+- family-names: "Natarajan"
+  given-names: "Iniyan"
+  orcid: "https://orcid.org/0000-0001-8242-4373"
+- family-names: "Paine"
+  given-names: "Scott N."
+  orcid: "https://orcid.org/0000-0003-4622-5857"
 - family-names: "Palumbo"
   given-names: "Daniel C. M."
   orcid: "https://orcid.org/0000-0002-7179-3816"
-- family-names: "Raymond"
-  given-names: "Alexander W."
-  orcid: "https://orcid.org/0000-0002-5779-4767"
-- family-names: "Wielgus"
-  given-names: "Maciek"
-  orcid: "https://orcid.org/0000-0002-8635-4242"
-title: "ngEHT simulation tools"
-version: 0.1
-date-released: 2021-09-20
+- family-names: "Roelofs"
+  given-names: "Freek"
+  orcid: "https://orcid.org/0000-0001-5461-3687"
+- family-names: "Tiede"
+  given-names: "Paul"
+  orcid: "https://orcid.org/0000-0003-3826-5648"
+title: "ngehtsim"
+version: 1.0.0
+date-released: 2023-12-29
 url: "https://github.com/Smithsonian/ngehtsim"

README.md

@@ -2,7 +2,8 @@
 
 [![Documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://smithsonian.github.io/ngehtsim/)
 [![Build status](https://github.com/Smithsonian/ngehtsim/actions/workflows/run_unit_tests.yml/badge.svg)](https://github.com/Smithsonian/ngehtsim/actions)
-[![Python versions](https://img.shields.io/badge/python-3.8|3.9|3.10-blue.svg)](https://github.com/Smithsonian/ngehtsim)
+[![Python versions](https://img.shields.io/badge/python-3.8|3.9|3.10|3.11-blue.svg)](https://github.com/Smithsonian/ngehtsim)
+[![Code coverage](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/dpesce/de229c48256d967a1cb8b29dbf575602/raw/covbadge.json)](https://github.com/Smithsonian/ngehtsim/actions)
 
 A set of tools for generating synthetic data for the Event Horizon Telescope ([EHT](https://eventhorizontelescope.org/)), the next-generation Event Horizon Telescope ([ngEHT](https://www.ngeht.org)), and other very long baseline interferometric arrays of radio telescopes.
 
@@ -24,6 +25,12 @@ ngehtsim is only tested on Python 3.8 and higher, and it may break for earlier v
     (.venv) $ pip install ./ngehtsim
 ```
 
+There is an optional calibration functionality that requires some additional dependencies; it can be installed using:
+
+```
+    (.venv) $ pip install ./ngehtsim[calib]
+```
+
 ## Checking that it works
 
 There are a number of example scripts contained in the [examples](./examples/) folder.  You can check to make sure your ngehtsim installation is working by running one of these scripts, e.g.:

docs/source/api.rst

@@ -9,4 +9,5 @@ Individual package documentation organized by area.
    ./obsgen
    ./metrics
    ./weather
+   ./calibration
 

docs/source/calibration.rst

@@ -0,0 +1,9 @@
+.. module:: calibration
+
+Calibration utilities
+=========================
+
+Definition of the calibration interface.
+
+.. automodule:: calibration.calibration
+   :members:

docs/source/installation.rst

@@ -15,6 +15,12 @@ To install ngehtsim, run pip from the main directory:
 
    $ pip install [--upgrade] . [--user]
 
+If you would like to additionally install the calibration dependencies, run:
+
+.. code-block:: console
+
+   $ pip install [--upgrade] .[calib] [--user]
+
 Dependencies
 ------------------------
 
@@ -26,7 +32,13 @@ ngehtsim uses the following packages:
 * `matplotlib <https://matplotlib.org>`_
 * `scipy <https://www.scipy.org>`_
 * `astropy <https://www.astropy.org/>`_
+* `ngEHTforecast <https://aeb.github.io/ngEHTforecast/html/docs/src/index.html>`_
+
+ngehtsim also has the option to include additional calibration capabilities during installation, which further requires:
+
+* `pandas <https://pandas.pydata.org/>`_
+* `eat <https://github.com/sao-eht/eat.git>`_
 
-Generating a local version of the documation for ngehtsim requires:
+Dependencies are specified in setup.py and will be handled via the pip install process. Generating a local version of the documentation for ngehtsim requires:
 
 * `Sphinx <https://www.sphinx-doc.org>`_

examples/example_SYMBA_export/generate_observation.py

@@ -22,10 +22,10 @@
 
 # generate a symmetric Gaussian model object
 mod = eh.model.Model()
-mod = mod.add_circ_gauss(F0=1.0,FWHM=40.0*eh.RADPERUAS)
+mod = mod.add_circ_gauss(F0=1.0, FWHM=40.0*eh.RADPERUAS)
 
 # save an image of the model
-im = mod.make_image(500.0*eh.RADPERUAS,512)
+im = mod.make_image(500.0*eh.RADPERUAS, 512)
 imfilename = '000000-I-model.fits'
 im.save_fits(imfilename)
 
@@ -34,14 +34,14 @@
 obsgen = og.obs_generator(settings)
 
 # generate and save the observation
-obs = obsgen.make_obs(im,addnoise=addnoise,addgains=addgains)
+obs = obsgen.make_obs(im, addnoise=addnoise, addgains=addgains)
 obs.save_uvfits('example_dataset.uvfits')
 
 # export SYMBA-compatible input files
 master_input_args = {'rpicard_path': rpicard_path,
                      'meqsilhouette_path': meqsilhouette_path,
                      'add_thermal_noise': str(addnoise)}
-obsgen.export_SYMBA(symba_workdir=symba_workdir,master_input_args=master_input_args,use_two_letter=use_two_letter)
+obsgen.export_SYMBA(symba_workdir=symba_workdir, master_input_args=master_input_args, use_two_letter=use_two_letter)
 
 # move image file to SYMBA working directory
 os.system('mv ' + imfilename + ' ' + symba_workdir + '/symba_input/' + imfilename)

examples/example_data_generation/generate_observation.py

@@ -1,8 +1,6 @@
 #######################################################
 # imports
 
-import numpy as np
-import ehtim as eh
 import ngehtsim.obs.obs_generator as og
 import ngehtsim.obs.obs_plotter as op
 import ngehtsim.metrics as cm
@@ -25,37 +23,37 @@
 #######################################################
 # make some plots of the data
 
-op.plot_uv(obs,filename='./example_plot_uv.png')
-op.plot_amp(obs,filename='./example_plot_amp.png')
-op.plot_phase(obs,filename='./example_plot_phase.png')
-op.plot_snr(obs,filename='./example_plot_snr.png')
+op.plot_uv(obs, filename='./example_plot_uv.png')
+op.plot_amp(obs, filename='./example_plot_amp.png')
+op.plot_phase(obs, filename='./example_plot_phase.png')
+op.plot_snr(obs, filename='./example_plot_snr.png')
 
 #######################################################
 # compute various metrics
 
 # compute FF metric
-ff = cm.calc_ff(obs,fov=200.0)
-print('FF metric value is: ',ff)
+ff = cm.calc_ff(obs, fov=200.0)
+print('FF metric value is: ', ff)
 
 # compute BFF metric for each Stokes parameter
-for stokes in ['I','Q','U','V']:
-    bff = cm.calc_bff(obs,fov=200.0,stokes=stokes)
-    print('Stokes ' + stokes + ' BFF metric value is: ',bff)
+for stokes in ['I', 'Q', 'U', 'V']:
+    bff = cm.calc_bff(obs, fov=200.0, stokes=stokes)
+    print('Stokes ' + stokes + ' BFF metric value is: ', bff)
 
 # compute LCG metric
 lcg = cm.calc_lcg(obs)
-print('LCG metric value is: ',lcg)
+print('LCG metric value is: ', lcg)
 
 # compute PSS metric
 pss = cm.calc_pss(obs)
-print('PSS metric value (in Jy) is: ',pss)
+print('PSS metric value (in Jy) is: ', pss)
 
 # compute angular resolution metric with different weightings
-for weighting in ['natural','uniform','robust']:
-    ar = cm.calc_ar(obs,artype='mean',weighting=weighting)
-    print('Average beam size (in uas) with ' + weighting + ' weighting is: ',ar)
+for weighting in ['natural', 'uniform', 'robust']:
+    ar = cm.calc_ar(obs, artype='mean', weighting=weighting)
+    print('Average beam size (in uas) with ' + weighting + ' weighting is: ', ar)
 
 #######################################################
 # plot a metric versus time for the observation
 
-op.plot_snapshot(obs,obsgen,'FF',fov=200.0,filename='./example_plot_FF.png')
+op.plot_snapshot(obs, obsgen, 'FF', fov=200.0, filename='./example_plot_FF.png')

examples/example_data_generation/settings.yaml

@@ -1,7 +1,7 @@
 ############################################################
 # input files
 
-model_file: '../data_files/M87_230GHz_Chael.fits'
+model_file: '../data_files/M87_230GHz.fits'
 
 ############################################################
 # observation specs