Transits across oblate stars

.github/workflows/tests.yml

@@ -28,9 +28,10 @@ jobs:
           - python-version: "3.9"
             pymc-version: "pymc3==3.11"
             arviz-version: ""
-          - python-version: "3.8"
-            pymc-version: "https://github.com/pymc-devs/pymc3/archive/main.zip"
-            arviz-version: ""
+          # TODO:
+          # - python-version: "3.8"
+          #  pymc-version: "https://github.com/pymc-devs/pymc3/archive/main.zip"
+          #  arviz-version: ""
 
     steps:
       - uses: actions/checkout@v2
@@ -61,27 +62,12 @@ jobs:
         run: |
           python -m pip install -U pip
           python -m pip install ${{ matrix.pymc-version }} ${{ matrix.arviz-version }}
-          python -m pip install -e ".[tests]"
-
-      - name: Run tests (greedy)
-        if: steps.install.outcome == 'success'
-        shell: bash -l {0}
-        run: python -m pytest -v tests/greedy --junitxml=junit/test-results-greedy.xml --cov=starry --cov-append
-
-      - name: Run tests (lazy)
-        if: steps.install.outcome == 'success'
-        shell: bash -l {0}
-        run: python -m pytest -v tests/lazy --junitxml=junit/test-results-lazy.xml --cov=starry --cov-append
-
-      - name: Run extension tests (greedy)
-        if: steps.install.outcome == 'success'
-        shell: bash -l {0}
-        run: python -m pytest -v starry/extensions/tests/greedy --junitxml=junit/test-results-extensions-greedy.xml --cov=starry --cov-append
+          STARRY_UNIT_TESTS=1 python -m pip install -e ".[tests]"
 
-      - name: Run extension tests (lazy)
+      - name: Run tests
         if: steps.install.outcome == 'success'
         shell: bash -l {0}
-        run: python -m pytest -v starry/extensions/tests/lazy --junitxml=junit/test-results-extensions-lazy.xml --cov=starry --cov-append
+        run: python -m pytest -v --junitxml=junit/test-results.xml --cov=starry
 
       - name: Get unique id
         id: unique-id
@@ -97,7 +83,7 @@ jobs:
         if: always()
         with:
           files: junit/test-*.xml
-          comment_on_pr: false
+          comment_mode: off
 
       - name: Coveralls
         uses: AndreMiras/coveralls-python-action@develop

.pre-commit-config.yaml

@@ -14,11 +14,10 @@ repos:
   rev: 19.3b0
   hooks:
   - id: black
-    language_version: python3.7
     exclude: lib
 
 - repo: https://github.com/dfm/black_nbconvert
-  rev: stable
+  rev: v0.3.0
   hooks:
   - id: black_nbconvert
     exclude: lib

docs/MapFactory.rst

@@ -15,3 +15,4 @@ arguments passed to it.
     LimbDarkenedMap
     RadialVelocityMap
     ReflectedLightMap
+    OblateMap

docs/OblateMap.rst

@@ -0,0 +1,7 @@
+Oblate Maps
+===========
+
+.. autoclass:: starry._OblateMap()
+    :noindex:
+    :members:
+    :inherited-members:

docs/hacks.py

@@ -64,17 +64,22 @@ class _RadialVelocityMap(CustomBase, starry.maps.RVBase, starry.maps.MapBase):
     __doc__ = starry.maps.RVBase.__doc__
 
 
+class _OblateMap(CustomBase, starry.maps.OblateBase, starry.maps.MapBase):
+    __doc__ = starry.maps.OblateBase.__doc__
+
+
 starry._SphericalHarmonicMap = _SphericalHarmonicMap
 starry._LimbDarkenedMap = _LimbDarkenedMap
 starry._ReflectedLightMap = _ReflectedLightMap
 starry._RadialVelocityMap = _RadialVelocityMap
-
+starry._OblateMap = _OblateMap
 
 replace = {
     "_SphericalHarmonicMap": "Map",
     "_LimbDarkenedMap": "Map",
     "_ReflectedLightMap": "Map",
     "_RadialVelocityMap": "Map",
+    "_OblateMap": "Map",
 }
 
 

notebooks/todo/EasySampling.ipynb

@@ -0,0 +1,203 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%run ../notebook_setup.py"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "import starry\n",
+    "import pymc3 as pm\n",
+    "import pymc3_ext as pmx"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Generate"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "map = starry.Map(oblate=True, lazy=False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "truths = {\n",
+    "    \"f\": 0.3,\n",
+    "    \"omega\": 0.5,\n",
+    "    \"inc\": 60,\n",
+    "    \"obl\": 30,\n",
+    "    \"b0\": 0.5,\n",
+    "    \"ro\": 0.1\n",
+    "}\n",
+    "\n",
+    "ferr = 3e-4"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "map.f = truths[\"f\"]\n",
+    "map.omega = truths[\"omega\"]\n",
+    "map.inc = truths[\"inc\"]\n",
+    "map.obl = truths[\"obl\"]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "xo = np.linspace(-1, 1, 300)\n",
+    "yo = truths[\"b0\"] * np.ones_like(xo)\n",
+    "ro = truths[\"ro\"]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fig, ax = plt.subplots(1)\n",
+    "ax.plot(xo, yo, \"k-\")\n",
+    "ax.plot(xo, yo - ro, \"k--\")\n",
+    "ax.plot(xo, yo + ro, \"k--\")\n",
+    "map.show(ax=ax)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "flux0 = map.flux(xo=xo, yo=yo, ro=ro)\n",
+    "flux = flux0 + ferr * np.random.randn(len(flux0))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "plt.plot(flux0);\n",
+    "plt.plot(flux, \"k.\", ms=3, alpha=0.75);"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Infer"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with pm.Model() as model:\n",
+    "    f = pm.Uniform(\"f\", lower=0.0, upper=0.9, testval=truths[\"f\"])\n",
+    "    omega = pm.Uniform(\"omega\", lower=0.0, upper=0.9, testval=truths[\"omega\"])\n",
+    "    inc = pm.Uniform(\"inc\", lower=0.0, upper=90.0, testval=truths[\"inc\"])\n",
+    "    obl = pm.Uniform(\"obl\", lower=-90, upper=90.0, testval=truths[\"obl\"])\n",
+    "    b0 = pm.Uniform(\"b0\", lower=-1.0, upper=1.0, testval=truths[\"b0\"])\n",
+    "    ro = pm.Uniform(\"ro\", lower=1e-5, upper=0.5, testval=truths[\"ro\"])\n",
+    "    map = starry.Map(oblate=True)\n",
+    "    map.f = f\n",
+    "    map.omega = omega\n",
+    "    map.inc = inc\n",
+    "    map.obl = obl\n",
+    "    yo = b0 * np.ones_like(xo)\n",
+    "    flux_model = map.flux(xo=xo, yo=yo, ro=ro)\n",
+    "    pm.Normal(\"obs\", mu=flux_model, sd=ferr, observed=flux)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "np.random.seed(42)\n",
+    "with model:\n",
+    "    trace = pmx.sample(\n",
+    "        tune=1000,\n",
+    "        draws=1000,\n",
+    "        chains=2,\n",
+    "        cores=1,\n",
+    "        target_accept=0.9,\n",
+    "        return_inferencedata=True,\n",
+    "    )"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pm.summary(trace)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pm.plot_trace(trace);"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}