Merge pull request #9 from JoranAngevaare/add_ci

Continuous integration
JelleAalbers · Aug 17, 2022 · 247a50b · 247a50b
2 parents fa7699a + 1ae5151
commit 247a50b
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diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -0,0 +1,59 @@
+name: Test package
+
+on:
+  workflow_dispatch:
+  release:
+    types: [ created ]
+  pull_request:
+  push:
+    branches:
+      - master
+
+jobs:
+  update:
+    name: "${{ matrix.test }}_py${{ matrix.python-version }}"
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: False
+      matrix:
+        python-version: [3.7, 3.8, 3.9, "3.10" ]
+        # Test coveralls (with numba disabled) and normal pytest
+        test: [ 'coveralls', 'pytest', ]
+        exclude:
+          - python-version: 3.7
+            test: pytest
+          - python-version: 3.9
+            test: pytest
+          - python-version: "3.10"
+            test: pytest
+    steps:
+      - name: Setup python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Checkout repo
+        uses: actions/checkout@v3
+      - name: Install requirements for tests and latest strax
+        run: |
+          # Requirements for running the notebooks as a pytest
+          pip install cython ipython
+          pip install nbconvert==6.4.3 nbmake pytest-xdist pytest coverage coveralls pytest-cov pytest-notebook ipython_genutils
+          # Several optional packages that are imported in the notebooks
+          pip install git+https://github.com/XENON1T/laidbax
+          python setup.py develop
+      - name: Test package
+        if: matrix.test == 'pytest'
+        run:
+          pytest --cov wimprates -v --nbmake notebooks/*.ipynb --durations 0 --nb-coverage
+      - name: Coveralls
+        env:
+          NUMBA_DISABLE_JIT: 1
+        if: matrix.test == 'coveralls'
+        run:
+          pytest --cov wimprates -v --nbmake notebooks/*.ipynb --durations 0 --nb-coverage
+      - name: Coveralls
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: coveralls --service=github
+      - name: goodbye
+        run: echo "tests done, bye bye"
diff --git a/notebooks/Checks, plots.ipynb b/notebooks/Checks, plots.ipynb
@@ -36,8 +36,10 @@
    "source": [
     "try:\n",
     "    plt.style.use('latex_thesis')\n",
+    "    _latex_thesis=True\n",
     "except (FileNotFoundError, OSError):\n",
-    "    print(\"Can't use my favourite plotting style... oh well\")"
+    "    print(\"Can't use my favourite plotting style... oh well\")\n",
+    "    _latex_thesis=False"
    ]
   },
   {
@@ -48,7 +50,8 @@
    "source": [
     "kms = nu.km/nu.s\n",
     "\n",
-    "from wimprates import v_0, v_earth, v_esc      \n",
+    "from wimprates import StandardHaloModel, v_earth\n",
+    "v_0, v_esc = StandardHaloModel().v_0, StandardHaloModel().v_esc\n",
     "\n",
     "def galactic_v_dist(v):\n",
     "    # Maxwell Boltzmann distribution with\n",
@@ -393,10 +396,16 @@
    ],
    "source": [
     "# Get mean energies and energy spectra\n",
-    "from laidbax import wimps\n",
-    "from s2only import wimprates as wr\n",
-    "\n",
-    "es = np.logspace(-2, 3.5, 500)\n",
+    "try:\n",
+    "    from laidbax import wimps\n",
+    "    from s2only import wimprates as wr\n",
+    "except ImportError:\n",
+    "    import wimprates as wr\n",
+    "    wimps = None\n",
+    "\n",
+    "es = np.logspace(-2, 3.5, 100)\n",
+    "# Reduce the number a bit to get the results quicker\n",
+    "mchi = mchi[::5]\n",
     "ms = mchi / gevcsq\n",
     "rates = []\n",
     "rates_bs = []\n",
@@ -407,7 +416,10 @@
     "means_bs = np.zeros(len(ms), dtype=np.float)\n",
     "\n",
     "for i, mw in enumerate(tqdm(ms)):\n",
-    "    r = wimps.wimp_recoil_spectrum(es, mass=mw, sigma=1e-45)\n",
+    "    if wimps is not None:\n",
+    "        r = wimps.wimp_recoil_spectrum(es, mass=mw, sigma=1e-45)\n",
+    "    else:\n",
+    "        r = wr.rate_wimp_std(es, mw, 1e-45)\n",
     "    rates.append(r)\n",
     "    rate_per_bin = (r[1:] + r[:-1])/2 * widths\n",
     "    if rate_per_bin.sum() != 0:\n",
@@ -435,9 +447,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from s2only.utils import load_pickle, dump_pickle\n",
-    "dump_pickle(dict(means=means, means_bs=means_bs, rates=rates, rates_bs=rates_bs, ms=ms),\n",
-    "            'dm_mean_energies.pickle')"
+    "try:\n",
+    "    from s2only.utils import load_pickle, dump_pickle\n",
+    "except ModuleNotFoundError:\n",
+    "    pass\n",
+    "else:\n",
+    "    dump_pickle(dict(means=means, means_bs=means_bs, rates=rates, rates_bs=rates_bs, ms=ms),\n",
+    "                'dm_mean_energies.pickle')"
    ]
   },
   {
@@ -461,7 +477,7 @@
     "    ax.set_ylabel(label, color=color)\n",
     "    ax.tick_params('y', colors=color)\n",
     "\n",
-    "v = v_earth + v_esc\n",
+    "v = v_earth() + v_esc\n",
     "plt.plot(mchi / gevcsq, \n",
     "         4 * mchi * mn / (mchi + mn)**2 * (mchi * v**2 /2) / nu.keV,\n",
     "        linestyle=':', c='b'\n",
@@ -574,13 +590,13 @@
     "tyear = 1e3 * 365\n",
     "\n",
     "plt.plot(ms, [tyear * total_rate(m, threshold=5) for m in ms], \n",
-    "         label='NR, $E_T =\\SI{5}{keV}$', \n",
+    "         label='NR, $E_T =\\SI{5}{keV}$' if _latex_thesis else 'NR, $E_T =5$ keV', \n",
     "         c='blue', linewidth=1)\n",
     "plt.plot(ms, [tyear * total_rate(m, threshold=1) for m in ms], \n",
-    "         label='NR, $E_T = \\SI{1}{keV}$', \n",
+    "         label='NR, $E_T = \\SI{1}{keV}$' if _latex_thesis else 'NR, $E_T = 1$ keV', \n",
     "         c='g', linewidth=1)\n",
     "plt.plot(ms, [tyear * total_rate(m, bs=True, threshold=0.18) * 1e-10 for m in ms], \n",
-    "         label='BS, $E_T =\\SI{180}{eV}$',\n",
+    "         label='BS, $E_T =\\SI{180}{eV}$' if _latex_thesis else 'BS, $E_T =180$ eV',\n",
     "         c='r', linewidth=1)\n",
     "plt.yscale('log')\n",
     "plt.ylim(None, 1e4)\n",
@@ -589,8 +605,12 @@
     "leg = plt.legend(loc='upper right')\n",
     "leg.get_frame().set_linewidth(0.0)\n",
     "leg.get_frame().set_alpha(0.85)\n",
-    "plt.ylabel('Rate (\\si{events/(ton\\;year)})')\n",
-    "plt.xlabel('$m_\\chi$ (\\si{GeV/c^2})')\n",
+    "if _latex_thesis:\n",
+    "    plt.ylabel('Rate (\\si{events/(ton\\;year)})')\n",
+    "    plt.xlabel('$m_\\chi$ (\\si{GeV/c^2})')\n",
+    "else:\n",
+    "    plt.ylabel('Rate')\n",
+    "    plt.xlabel('$m_\\chi$')\n",
     "plt.gca().invert_yaxis()\n",
     "#plt.plot(es, total_rate(, c='b', label='$\\SI{1}{GeV/c^2}$')\n",
     "plt.xlim(1e-1, 1e4)\n",
@@ -615,10 +635,10 @@
     }
    ],
    "source": [
-    "plt.plot(es, nearest_rate(1), c='b', label='$\\SI{1}{GeV/c^2}$')\n",
-    "plt.plot(es, nearest_rate(100), label='$\\SI{100}{GeV/c^2}$', c='g')\n",
+    "plt.plot(es, nearest_rate(1), c='b', label='$\\SI{1}{GeV/c^2}$' if _latex_thesis else None)\n",
+    "plt.plot(es, nearest_rate(100), label='$\\SI{100}{GeV/c^2}$' if _latex_thesis else None, c='g')\n",
     "plt.plot(es, nearest_rate(1, bs=True) * 1e-10, c='b', linestyle=':',\n",
-    "         label='$\\SI{1}{GeV/c^2}$, Bremsstrahlung' # $\\\\times 10^{10}$'\n",
+    "         label='$\\SI{1}{GeV/c^2}$, Bremsstrahlung'  if _latex_thesis else None # $\\\\times 10^{10}$'\n",
     "        )\n",
     "leg = plt.legend(loc='upper right', frameon=False)\n",
     "#leg.get_frame().set_linewidth(0.0)\n",
@@ -695,7 +715,7 @@
  "metadata": {
   "anaconda-cloud": {},
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -709,7 +729,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.7"
+   "version": "3.10.4"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/DM-electron scattering.ipynb b/notebooks/DM-electron scattering.ipynb
@@ -325,11 +325,13 @@
     "    \n",
     "    for shell, rn in drsn.items():\n",
     "        rn *= (1000 * nu.kg * nu.year)\n",
-    "        plt.plot(n_el, rn, linestyle='steps-mid', label=shell)\n",
+    "        plt.plot(n_el, rn, drawstyle='steps-mid', label=shell)\n",
     "\n",
     "    plt.plot(n_el, np.sum(list(drsn.values()), axis=0),\n",
     "             label='Total',\n",
-    "             drawstyle='steps-mid', linestyle='--', c='k')\n",
+    "             drawstyle='steps-mid', \n",
+    "             linestyle='--', \n",
+    "             c='k')\n",
     "\n",
     "    plt.title(title + (' -- SWAP 4s<->4p' if do_swap else ''))\n",
     "    plt.legend(loc='upper right', ncol=2)\n",
@@ -355,7 +357,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -369,7 +371,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.7"
+   "version": "3.10.4"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/Spin-dependent.ipynb b/notebooks/Spin-dependent.ipynb
@@ -3,9 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "import numpy as np\n",
@@ -32,9 +30,7 @@
   {
    "cell_type": "code",
    "execution_count": 2,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "name": "stderr",
@@ -48,16 +44,14 @@
    "source": [
     "try:\n",
     "    plt.style.use('latex_thesis')\n",
-    "except FileNotFoundError:\n",
+    "except (FileNotFoundError, OSError):\n",
     "    print(\"Can't use my favourite plotting style... oh well\")"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 5,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -76,7 +70,6 @@
    "cell_type": "code",
    "execution_count": 8,
    "metadata": {
-    "collapsed": false,
     "scrolled": false
    },
    "outputs": [],
@@ -122,9 +115,7 @@
   {
    "cell_type": "code",
    "execution_count": 9,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -184,9 +175,7 @@
   {
    "cell_type": "code",
    "execution_count": 10,
-   "metadata": {
-    "collapsed": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -265,7 +254,7 @@
  "metadata": {
   "anaconda-cloud": {},
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -279,7 +268,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.4.5"
+   "version": "3.10.4"
   }
  },
  "nbformat": 4,