Fix yml files, add test, add workflow (#1)

* Test parsing of yaml files, and add workflow * fix workflow * fix workflow * fix yml formatting
mfschubert · Nov 23, 2024 · 733e360 · 733e360
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diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -0,0 +1,25 @@
+name: CI
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+  schedule:
+      - cron: "0 13 * * 1"  # Every Monday at 9AM EST
+
+jobs:
+  test-parsing:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up environment
+        run: |
+          python -m pip install --upgrade pip
+          pip install parameterized
+          pip install pytest
+
+      - name: Run tests
+        run: pytest
diff --git a/database/data-nk/main/CdSe/Ninomiya-cubic.yml b/database/data-nk/main/CdSe/Ninomiya-cubic.yml
@@ -2,8 +2,9 @@
 # refractiveindex.info database is in the public domain
 # copyright and related rights waived via CC0 1.0
 
-REFERENCES: "1) S. Ninomiya and S. Adachi. Optical properties of cubic and hexagonal CdSe, <a href="https://doi.org/10.1063/1.359815"><i>J. Appl. Phys.</i> <b>78</b>, 4681-4689 (1995)</a><br>2) Y. D. Kim, M. V. Klein, S. F. Ren, Y. C. Chang, H. Luo, N. Samarth, J. K. Furdyna.
-Optical properties of zinc-blende CdSe and Zn<sub>x</sub>Cd<sub>1−x</sub>Se films grown on GaAs, <a href="https://doi.org/10.1103/PhysRevB.49.7262"><i>Phys. Rev. B</i> <b>49</b>, 7262-7270 (1994)</a><br>* Authors of Ref. 1 provide a simplified model of the interband transitions (MDF) based on the experimental data from Ref. 2.<br>[<a href="https://github.com/polyanskiy/refractiveindex.info-scripts/blob/master/scripts/Ninomiya%201995%20-%20cubic%20CdSe.py">Calculation script (Python)</a>]"
+REFERENCES: |
+    "1) S. Ninomiya and S. Adachi. Optical properties of cubic and hexagonal CdSe, <a href="https://doi.org/10.1063/1.359815"><i>J. Appl. Phys.</i> <b>78</b>, 4681-4689 (1995)</a><br>2) Y. D. Kim, M. V. Klein, S. F. Ren, Y. C. Chang, H. Luo, N. Samarth, J. K. Furdyna.
+    Optical properties of zinc-blende CdSe and Zn<sub>x</sub>Cd<sub>1−x</sub>Se films grown on GaAs, <a href="https://doi.org/10.1103/PhysRevB.49.7262"><i>Phys. Rev. B</i> <b>49</b>, 7262-7270 (1994)</a><br>* Authors of Ref. 1 provide a simplified model of the interband transitions (MDF) based on the experimental data from Ref. 2.<br>[<a href="https://github.com/polyanskiy/refractiveindex.info-scripts/blob/master/scripts/Ninomiya%201995%20-%20cubic%20CdSe.py">Calculation script (Python)</a>]"
 COMMENTS: |
     Cubic CdSe. Room temperature.
 DATA:

diff --git a/database/data-nk/main/InP/Pettit.yml b/database/data-nk/main/InP/Pettit.yml
@@ -2,8 +2,9 @@
 # refractiveindex.info database is in the public domain
 # copyright and related rights waived via CC0 1.0
 
-REFERENCES: "1) G. D. Pettit and W. J. Turner. Refractive index of InP, <a href="https://doi.org/10.1063/1.1714410"><i>J. Appl. Phys.</i> <b>36</b>, 2081 (1965)</a><br>2) A. N. Pikhtin and A. D. Yas’kov. Disperson of the refractive index
-of semiconductors with diamond and zinc-blende structures, <i>Sov. Phys. Semicond.</i> <b>12</b>, 622-626 (1978) (as cited in Handbook of Optics, 2nd edition, Vol. 2. McGraw-Hill 1994)<br>3) Handbook of Optics, 2nd edition, Vol. 2. McGraw-Hill 1994<br> * Ref. 3 provides a Sellmeier equation based on data from Ref. 1 and Ref. 2."
+REFERENCES: |
+    "1) G. D. Pettit and W. J. Turner. Refractive index of InP, <a href="https://doi.org/10.1063/1.1714410"><i>J. Appl. Phys.</i> <b>36</b>, 2081 (1965)</a><br>2) A. N. Pikhtin and A. D. Yas’kov. Disperson of the refractive index
+    of semiconductors with diamond and zinc-blende structures, <i>Sov. Phys. Semicond.</i> <b>12</b>, 622-626 (1978) (as cited in Handbook of Optics, 2nd edition, Vol. 2. McGraw-Hill 1994)<br>3) Handbook of Optics, 2nd edition, Vol. 2. McGraw-Hill 1994<br> * Ref. 3 provides a Sellmeier equation based on data from Ref. 1 and Ref. 2."
 COMMENTS: |
     Room temperature
 DATA:

diff --git a/database/data-nk/main/Si/Schinke.yml b/database/data-nk/main/Si/Schinke.yml
@@ -2,8 +2,9 @@
 # refractiveindex.info database is in the public domain
 # copyright and related rights waived via CC0 1.0
 
-REFERENCES: "1) C. Schinke, P. C. Peest, J. Schmidt, R. Brendel,  K. Bothe, M. R. Vogt, I. Kröger, S. Winter, A. Schirmacher, S. Lim, H. T. Nguyen, D. MacDonald. Uncertainty analysis for the coefficient of band-to-band absorption of crystalline silicon.
-<a href="https://doi.org/10.1063%2F1.4923379"><i>AIP Advances</i> <b>5</b>, 67168 (2015)</a><br>2) M. R. Vogt. <i>Development of physical models for the simulation of optical properties of solar cell modules</i>, <a href="https://www.tib.eu/en/search/id/TIBKAT%3A852464657">PhD. Thesis (2015)</a>"
+REFERENCES: |
+    "1) C. Schinke, P. C. Peest, J. Schmidt, R. Brendel,  K. Bothe, M. R. Vogt, I. Kröger, S. Winter, A. Schirmacher, S. Lim, H. T. Nguyen, D. MacDonald. Uncertainty analysis for the coefficient of band-to-band absorption of crystalline silicon.
+    <a href="https://doi.org/10.1063%2F1.4923379"><i>AIP Advances</i> <b>5</b>, 67168 (2015)</a><br>2) M. R. Vogt. <i>Development of physical models for the simulation of optical properties of solar cell modules</i>, <a href="https://www.tib.eu/en/search/id/TIBKAT%3A852464657">PhD. Thesis (2015)</a>"
 COMMENTS: |
     Relative uncertainties of the absorption coefficient: 0.4% at 0.250 µm, 11% at 0.6 µm, 1.4% at 1 µm, 12% at 1.2 µm and 180% at 1.45 µm. Temperature: 295 K.
 DATA:

diff --git a/database/data-nk/main/SiO2/Malitson.yml b/database/data-nk/main/SiO2/Malitson.yml
@@ -2,8 +2,9 @@
 # refractiveindex.info database is in the public domain
 # copyright and related rights waived via CC0 1.0
 
-REFERENCES: "1) I. H. Malitson. Interspecimen comparison of the refractive index of fused silica, <a href="https://doi.org/10.1364/JOSA.55.001205"><i>J. Opt. Soc. Am.</i> <b>55</b>, 1205-1208 (1965)</a><br>2) C. Z. Tan. Determination of refractive index of silica glass for infrared wavelengths by IR spectroscopy, <a href="https://doi.org/10.1016/S0022-3093(97)00438-9"><i>J. Non-Cryst. Solids</i> <b>223</b>, 158-163 (1998)</a><br>
-<sup>*</sup> Sellmeier formula is reported in Ref. 1 for the 0.21-3.71 μm wavelength range. Ref. 2 verifies the validity of the formula up to 6.7 μm."
+REFERENCES: |
+    "1) I. H. Malitson. Interspecimen comparison of the refractive index of fused silica, <a href="https://doi.org/10.1364/JOSA.55.001205"><i>J. Opt. Soc. Am.</i> <b>55</b>, 1205-1208 (1965)</a><br>2) C. Z. Tan. Determination of refractive index of silica glass for infrared wavelengths by IR spectroscopy, <a href="https://doi.org/10.1016/S0022-3093(97)00438-9"><i>J. Non-Cryst. Solids</i> <b>223</b>, 158-163 (1998)</a><br>
+    <sup>*</sup> Sellmeier formula is reported in Ref. 1 for the 0.21-3.71 μm wavelength range. Ref. 2 verifies the validity of the formula up to 6.7 μm."
 COMMENTS: |
     Fused silica, 20 °C
 DATA:

diff --git a/tests/test_parse.py b/tests/test_parse.py
@@ -0,0 +1,22 @@
+"""Tests that all files can be parsed."""
+
+import pathlib
+import unittest
+import yaml
+from parameterized import parameterized
+
+DATABASE_PATH = pathlib.Path(__file__).resolve().parent.parent / "database"
+PATHS = list(DATABASE_PATH.rglob("*.yml"))
+
+
+def custom_name_func(testcase_func, param_num, param):
+    del param_num
+    path = str(param.args[0])
+    return f"{testcase_func.__name__}{parameterized.to_safe_name(path)}"
+
+
+class ParseTest(unittest.TestCase):
+    @parameterized.expand(PATHS, name_func=custom_name_func)
+    def test_can_parse(self, path):
+        with open(path, "r") as stream:
+            yaml.safe_load(stream)