Update colors

.github/workflows/test_notebook.yml

@@ -7,22 +7,29 @@ on:
   pull_request:
     branches: 
       - main
+      - NG20
 
 jobs:
   build:
+    runs-on: ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest] # Once we get the tex packages changed, we should include "macos-13"
         python-version: ["3.9", "3.10", "3.11", "3.12"]
+        os: [ubuntu-latest] # Once we get the tex packages changed, we should include "macos-13"
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
+    - name: Install Required Ubuntu Packages
     - name: Install Required Ubuntu Packages
       run: |
         sudo apt-get update
         sudo apt-get install texlive-latex-base cm-super-minimal pdftk latex2html
     - uses: actions/checkout@v4
+    - uses: mamba-org/setup-micromamba@v1
+    - uses: actions/checkout@v4
     - uses: mamba-org/setup-micromamba@v1
       with:
           init-shell: bash
@@ -49,6 +56,31 @@ jobs:
             jupyter
             seaborn
             gitpython
+    - name: Install Main Code
+          init-shell: bash
+          environment-name: pulsar
+          cache-environment: true
+          cache-downloads: true
+          create-args: >-
+            -c conda-forge
+            python=${{ matrix.python-version }}
+            pytest
+            cython
+            pint-pulsar
+            tempo2
+            libstempo
+            enterprise-pulsar
+            enterprise_extensions
+            scikit-sparse
+            scikit-learn
+            ruamel.yaml
+            nbconvert
+            ipywidgets>=7.6.3
+            weasyprint
+            pytest-xdist>=2.3.0
+            jupyter
+            seaborn
+            gitpython
     - name: Install Main Code
       shell: bash -el {0}
       run: |
@@ -61,13 +93,18 @@ jobs:
         pytest tests/test_run_notebook.py -k $PULSAR_NAME
         ls -lah
         mv tmp* nb_outputs
+        export JUPYTER_PLATFORM_DIRS=1
+        pytest tests/test_run_notebook.py -k $PULSAR_NAME
+        ls -lah
+        mv tmp* nb_outputs
     - name: Archive Notebook Output Files
+      uses: actions/upload-artifact@v4
       uses: actions/upload-artifact@v4
       with:
+        name: TestNB-OutputFiles_${{ matrix.python-version }}_${{ matrix.os }}_${{ steps.date.outputs.date }}
         name: TestNB-OutputFiles_${{ matrix.python-version }}_${{ matrix.os }}_${{ steps.date.outputs.date }}
         path: |
           nb_outputs/*/*.pdf
           nb_outputs/*/*.tim
           nb_outputs/*/*.par
         compression-level: 6
-

nb_templates/process_v1.1.ipynb

@@ -262,7 +262,7 @@
     "        # to temporarily address current inconsistency between enterprise <= v3.1.0 and pint implementations\n",
     "        mo_new = lu.convert_enterprise_equads(mo_new)\n",
     "        \n",
-    "    except OSError as e:\n",
+    "    except (OSError, ValueError) as e:\n",
     "        log.warning(f\"Unable to read noise chains from {tc.get_noise_dir()}: {e}\")\n",
     "    else:\n",
     "        mo = mo_new\n",

nb_templates/process_v1.2.ipynb

@@ -48,7 +48,6 @@
     "autorun = False\n",
     "run_Ftest = True  # Set to False if you don't need F-tests and want a faster notebook run!\n",
     "check_excision = True\n",
-    "num_noise_iter = 2e5\n",
     "\n",
     "if not autorun:\n",
     "    run_noise_analysis = False \n",
@@ -257,12 +256,17 @@
     "if run_noise_analysis or use_existing_noise_dir:\n",
     "    mo_new = copy.deepcopy(mo)\n",
     "    lu.remove_noise(mo_new)\n",
-    "    nu.model_noise(mo_new, to, using_wideband = using_wideband, run_noise_analysis = run_noise_analysis, n_iter = num_noise_iter)\n",
+    "    nu.model_noise(mo_new, to,\n",
+    "                   using_wideband = using_wideband,\n",
+    "                   run_noise_analysis = run_noise_analysis,\n",
+    "                   model_kwargs=tc.config['noise_run']['model'],\n",
+    "                   sampler_kwargs=tc.config['noise_run']['inference'],\n",
+    "    )\n",
     "    try:\n",
     "        mo_new = nu.add_noise_to_model(mo_new, using_wideband = using_wideband, base_dir=tc.get_noise_dir(), \n",
     "                                       compare_dir=tc.get_compare_noise_dir(), no_corner_plot=tc.get_no_corner())\n",
     "        \n",
-    "    except OSError as e:\n",
+    "    except (OSError, ValueError) as e:\n",
     "        log.warning(f\"Unable to read noise chains from {tc.get_noise_dir()}: {e}\")\n",
     "    else:\n",
     "        mo = mo_new\n",

pyproject.toml

@@ -13,6 +13,7 @@ authors = [
   { name="Anne Archibald", email="anne.archibald@nanograv.org" },
   { name="Kevin Wilson", email="kevin.wilson@nanograv.org" },
   { name="Ross Jennings", email="ross.jennings@nanograv.org" },
+  { name="Jeremy Baier", email="jeremy.baier@nanograv.org"}
 ]
 description = "A long-lived repository for NANOGrav Pulsar Timing analysis work."
 readme = "README.md"
@@ -31,14 +32,19 @@ dependencies = [
     "pytest-xdist[psutil]>=2.3.0",
     "notebook",
     "seaborn",
-    "gitpython",
+    "la-forge",
+    "arviz",
+    "fastshermanmorrison-pulsar",
 ]
 classifiers = [
     "Programming Language :: Python :: 3",
     "License :: OSI Approved :: MIT License",
     "Operating System :: OS Independent",
 ]
 
+[tool.setuptools.package-data]
+pint_pal = ["defaults.yaml", "plot_settings.yaml"]
+
 [project.urls]
 "Homepage" = "https://github.com/nanograv/pint_pal"
 "Bug Tracker" = "https://github.com/nanograv/pint_pal/issues"

src/pint_pal/__init__.py

@@ -1,4 +1,6 @@
 import pint_pal.checkin
+import pint_pal.config
+from pint_pal.config import set_data_root, reset_data_root
 
 from . import _version
 __version__ = _version.get_versions()['version']

src/pint_pal/config.py

@@ -0,0 +1,69 @@
+from ruamel.yaml import YAML
+import os.path
+yaml = YAML(typ='safe')
+PACKAGE_DIR = os.path.dirname(__file__)
+DATA_ROOT = '.'
+
+def set_data_root(path):
+    """
+    Set the root directory of the data repository to be used with PINT Pal.
+    PINT Pal will search this directory for a configuration file specifying settings
+    such as the appropriate JPL ephemeris and version of TT(BIPM) to check for when
+    validating timing models.
+
+    It will also be treated as the base directory when resolving paths in YAML
+    configuration files. This allows notebooks (or scripts) using YAML files within
+    the data repository, which specify paths relative to the data root, to be run
+    from other locations.
+
+    The default value of `data_root` is '.' (the current working directory), which
+    is sufficient in cases where either (1) no data repository is in use, or
+    (2) all scripts and notebooks are run from the root of the data repository.
+    """
+    global DATA_ROOT
+    DATA_ROOT = os.path.realpath(os.path.expanduser(path))
+    try:
+        read_config_file(os.path.join(DATA_ROOT, 'pint_pal_project.yaml'))
+    except FileNotFoundError:
+        pass
+
+def reset_data_root():
+    """
+    Reset the data root and config variables to the default values.
+    """
+    global DATA_ROOT
+    DATA_ROOT = '.'
+    read_config_file(os.path.join(PACKAGE_DIR, 'defaults.yaml'))
+
+def read_config_file(config_file):
+    """
+    Read a configuration file, along the lines of `defaults.yaml`, and load the results
+    into a location that can be accessed by other PINT Pal code.
+    """
+    with open(config_file, 'r') as f:
+        config = yaml.load(f)
+
+    global LATEST_BIPM
+    global LATEST_EPHEM
+    global PLANET_SHAPIRO
+    global CORRECT_TROPOSPHERE
+    global FREQUENCY_RATIO
+    global MAX_SOLARWIND_DELAY
+    global LATEST_TOA_RELEASE
+
+    if 'LATEST_BIPM' in config:
+        LATEST_BIPM = config['LATEST_BIPM']
+    if 'LATEST_EPHEM' in config:
+        LATEST_EPHEM = config['LATEST_EPHEM']
+    if 'PLANET_SHAPIRO' in config:
+        PLANET_SHAPIRO = config['PLANET_SHAPIRO']
+    if 'CORRECT_TROPOSPHERE' in config:
+        CORRECT_TROPOSPHERE = config['CORRECT_TROPOSPHERE']
+    if 'FREQUENCY_RATIO' in config:
+        FREQUENCY_RATIO = config['FREQUENCY_RATIO']
+    if 'MAX_SOLARWIND_DELAY' in config:
+        MAX_SOLARWIND_DELAY = config['MAX_SOLARWIND_DELAY']
+    if 'LATEST_TOA_RELEASE' in config:
+        LATEST_TOA_RELEASE = config['LATEST_TOA_RELEASE']
+
+read_config_file(os.path.join(PACKAGE_DIR, 'defaults.yaml'))

src/pint_pal/defaults.yaml

@@ -0,0 +1,21 @@
+# Here we keep track of global default settings
+#
+# These can be overridden on a per-project basis by placing a file
+# called `pint_pal_project.yaml` in the `data_root` location (this
+# defaults to the current working directory, but can be configured
+# with `pint_pal.set_data_root()`).
+
+# Choice of clock, SSE
+LATEST_BIPM: "BIPM2021"    # latest clock realization to use
+LATEST_EPHEM: "DE440"      # latest solar system ephemeris to use
+
+# Toggle various corrections
+PLANET_SHAPIRO: True       # correct for Shapiro delay from planets
+CORRECT_TROPOSPHERE: True  # correct for tropospheric delays
+
+# DMX model defaults
+FREQUENCY_RATIO: 1.1       # set the high/low frequency ratio for DMX bins
+MAX_SOLARWIND_DELAY: 0.1   # set the maximum permited 'delay' from SW [us]
+
+# Desired TOA release tag
+LATEST_TOA_RELEASE: "2021.08.25-9d8d617"    # current set of TOAs available