From 7381a9e01093d2a91c8ed3426f01dc66bd415e0b Mon Sep 17 00:00:00 2001 From: Sean Kavanagh Date: Mon, 20 Nov 2023 23:06:38 +0000 Subject: [PATCH] Use `catch_warnings` instead of `redirect_stderr` to avoid odd behaviour on GitHub actions --- doped/analysis.py | 7 +++---- examples/CdTe/CdTe_example_dpd.json | 2 +- examples/YTOS/YTOS_example_dpd.json | 2 +- tests/data/Sb2Se3/Sb2Se3_O_example_dpd.json | 2 +- .../Sb2Se3/defect/Sb2Se3_defect_dict.json | 2 +- tests/test_analysis.py | 19 ++++++++++--------- 6 files changed, 17 insertions(+), 17 deletions(-) diff --git a/doped/analysis.py b/doped/analysis.py index 817f8be1..45537859 100644 --- a/doped/analysis.py +++ b/doped/analysis.py @@ -7,7 +7,6 @@ publication-quality outputs. """ import contextlib -import io import itertools import os import warnings @@ -1225,10 +1224,10 @@ def _multiprocess_parse_defect(self, defect_folder): Process defect and catch warnings along the way, so we can print which warnings came from which defect. """ - str_io = io.StringIO() # Redirect stderr to capture warnings - with contextlib.redirect_stderr(str_io): # capture warnings + with warnings.catch_warnings(record=True) as captured_warnings: parsed_defect_entry = self._parse_defect(defect_folder) - warnings_string = str_io.getvalue() + + warnings_string = "\n".join(str(warning.message) for warning in captured_warnings) return parsed_defect_entry, warnings_string diff --git a/examples/CdTe/CdTe_example_dpd.json b/examples/CdTe/CdTe_example_dpd.json index 10b6f5c8..9756dd6d 100644 --- a/examples/CdTe/CdTe_example_dpd.json +++ b/examples/CdTe/CdTe_example_dpd.json @@ -1 +1 @@ -{"@module": "doped.utils.legacy_pmg.thermodynamics", "@class": "DefectPhaseDiagram", "entries": [{"defect": {"@module": "doped.core", "@class": "Vacancy", "structure": {"@module": "pymatgen.core.structure", "@class": "Structure", "charge": 0.0, "lattice": {"matrix": [[13.086768, 0.0, 0.0], [0.0, 13.086768, 0.0], [0.0, 0.0, 13.086768]], "pbc": [true, true, true], 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b/tests/data/Sb2Se3/defect/Sb2Se3_defect_dict.json @@ -1 +1 @@ -{"O_Se_Cs_Sb2.00_+2": {"defect": {"@module": "doped.core", "@class": "Substitution", "structure": {"@module": "pymatgen.core.structure", "@class": "Structure", "charge": 0.0, "lattice": {"matrix": [[11.85764482, 0.0, 0.0], [0.0, 11.54591305, 0.0], [0.0, 0.0, 11.92814205]], "pbc": [true, true, true], "a": 11.85764482, "b": 11.54591305, "c": 11.92814205, "alpha": 90.0, "beta": 90.0, "gamma": 90.0, "volume": 1633.0501523241192}, "properties": {}, "sites": [{"species": [{"element": "Sb", "oxidation_state": 3.0, "spin": null, "occu": 1}], "abc": [0.25, 0.03729851, 0.14453757], "xyz": [2.964411205, 0.43064535335455545, 1.7240646665218184], "properties": {"selective_dynamics": [true, true, true]}, "label": "Sb"}, {"species": [{"element": "Sb", "oxidation_state": 3.0, "spin": null, "occu": 1}], "abc": [0.75, 0.17223023, 0.53227558], "xyz": [8.893233615, 1.9885552601615015, 6.349058727986138], "properties": {"selective_dynamics": 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{"selective_dynamics": [true, true, true]}, "label": "Sb"}, {"species": [{"element": "Sb", "occu": 1}], "abc": [0.58333333, 0.46270149, 0.64453757], "xyz": [6.916959438807851, 5.342311171645444, 7.688135691521818], "properties": {"selective_dynamics": [true, true, true]}, "label": "Sb"}, {"species": [{"element": "Sb", "occu": 1}], "abc": [0.91666667, 0.46270149, 0.64453757], "xyz": [10.86950779119215, 5.342311171645444, 7.688135691521818], "properties": {"selective_dynamics": [true, true, true]}, "label": "Sb"}, {"species": [{"element": "Sb", "occu": 1}], "abc": [0.58333333, 0.03729851, 0.14453757], "xyz": [6.916959438807851, 0.43064535335455545, 1.7240646665218184], "properties": {"selective_dynamics": [true, true, true]}, "label": "Sb"}, {"species": [{"element": "Sb", "occu": 1}], "abc": [0.91666667, 0.03729851, 0.14453757], "xyz": [10.86950779119215, 0.43064535335455545, 1.7240646665218184], "properties": {"selective_dynamics": [true, true, true]}, "label": "Sb"}, {"species": [{"element": "Sb", "occu": 1}], "abc": [0.41666667, 0.96270149, 0.85546243], "xyz": [4.94068538119215, 11.115267696645445, 10.20407738347818], "properties": {"selective_dynamics": [true, true, true]}, "label": "Sb"}, {"species": [{"element": "Sb", "occu": 1}], "abc": [0.08333333, 0.96270149, 0.85546243], "xyz": [0.9881370288078506, 11.115267696645445, 10.20407738347818], "properties": {"selective_dynamics": [true, true, true]}, "label": "Sb"}, {"species": [{"element": "Sb", "occu": 1}], "abc": [0.08333333, 0.53729851, 0.35546243], "xyz": [0.9881370288078506, 6.203601878354554, 4.2400063584781815], "properties": {"selective_dynamics": [true, true, true]}, "label": "Sb"}, {"species": [{"element": "Sb", "occu": 1}], "abc": [0.41666667, 0.53729851, 0.35546243], "xyz": [4.94068538119215, 6.203601878354554, 4.2400063584781815], "properties": {"selective_dynamics": [true, true, true]}, "label": "Sb"}, {"species": [{"element": "Sb", "occu": 1}], "abc": [0.75, 0.53729851, 0.35546243], "xyz": [8.893233615, 6.203601878354554, 4.2400063584781815], "properties": {"selective_dynamics": [true, true, true]}, "label": "Sb"}, {"species": [{"element": "Sb", "occu": 1}], "abc": [0.25, 0.46270149, 0.64453757], "xyz": [2.964411205, 5.342311171645444, 7.688135691521818], "properties": {"selective_dynamics": [true, true, true]}, "label": "Sb"}, {"species": [{"element": "Sb", "occu": 1}], "abc": [0.75, 0.96270149, 0.85546243], "xyz": [8.893233615, 11.115267696645445, 10.20407738347818], "properties": {"selective_dynamics": [true, true, true]}, "label": "Sb"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.58333333, 0.37211005, 0.44742291], "xyz": [6.916959438807851, 4.296350282331153, 5.336924026904366], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.08333333, 0.55514531, 0.87225883], "xyz": [0.9881370288078506, 6.4096594793752955, 10.404427228606801], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.91666667, 0.37211005, 0.44742291], "xyz": [10.86950779119215, 4.296350282331153, 5.336924026904366], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.08333333, 0.62788995, 0.55257709], "xyz": [0.9881370288078506, 7.249562767668848, 6.591218023095634], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.41666667, 0.62788995, 0.55257709], "xyz": [4.94068538119215, 7.249562767668848, 6.591218023095634], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.75, 0.62788995, 0.55257709], "xyz": [8.893233615, 7.249562767668848, 6.591218023095634], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.41666667, 0.55514531, 0.87225883], "xyz": [4.94068538119215, 6.4096594793752955, 10.404427228606801], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.41666667, 0.19228864, 0.20998203], "xyz": [4.94068538119215, 2.220147917942752, 2.5046954817873615], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.25, 0.12788995, 0.94742291], "xyz": [2.964411205, 1.4766062426688475, 11.300995051904366], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.58333333, 0.12788995, 0.94742291], "xyz": [6.916959438807851, 1.4766062426688475, 11.300995051904366], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.91666667, 0.12788995, 0.94742291], "xyz": [10.86950779119215, 1.4766062426688475, 11.300995051904366], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.08333333, 0.19228864, 0.20998203], "xyz": [0.9881370288078506, 2.220147917942752, 2.5046954817873615], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.75, 0.19228864, 0.20998203], "xyz": [8.893233615, 2.220147917942752, 2.5046954817873615], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.25, 0.44485469, 0.12774117], "xyz": [2.964411205, 5.136253570624704, 1.5237148213931984], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.25, 0.37211005, 0.44742291], "xyz": [2.964411205, 4.296350282331153, 5.336924026904366], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": 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[0.9881370288078506, 10.909210095624704, 4.440356203606801], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.41666667, 0.94485469, 0.37225883], "xyz": [4.94068538119215, 10.909210095624704, 4.440356203606801], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.75, 0.94485469, 0.37225883], "xyz": [8.893233615, 10.909210095624704, 4.440356203606801], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.25, 0.05514531, 0.62774117], "xyz": [2.964411205, 0.6367029543752954, 7.487785846393198], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.58333333, 0.05514531, 0.62774117], "xyz": [6.916959438807851, 0.6367029543752954, 7.487785846393198], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.58333333, 0.44485469, 0.12774117], "xyz": [6.916959438807851, 5.136253570624704, 1.5237148213931984], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.08333333, 0.30771136, 0.70998203], "xyz": [0.9881370288078506, 3.5528086070572478, 8.468766506787363], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.41666667, 0.30771136, 0.70998203], "xyz": [4.94068538119215, 3.5528086070572478, 8.468766506787363], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.75, 0.30771136, 0.70998203], "xyz": [8.893233615, 3.5528086070572478, 8.468766506787363], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.25, 0.69228864, 0.29001797], "xyz": [2.964411205, 7.993104442942752, 3.4593755432126385], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.58333333, 0.69228864, 0.29001797], "xyz": [6.916959438807851, 7.993104442942752, 3.4593755432126385], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.91666667, 0.69228864, 0.29001797], "xyz": [10.86950779119215, 7.993104442942752, 3.4593755432126385], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.25, 0.80771136, 0.79001797], "xyz": [2.964411205, 9.325765132057247, 9.423446568212638], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.58333333, 0.80771136, 0.79001797], "xyz": [6.916959438807851, 9.325765132057247, 9.423446568212638], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.91666667, 0.80771136, 0.79001797], "xyz": [10.86950779119215, 9.325765132057247, 9.423446568212638], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.41666667, 0.87211005, 0.05257709], "xyz": [4.94068538119215, 10.069306807331152, 0.6271469980956345], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}, {"species": [{"element": "Se", "occu": 1}], "abc": [0.91666667, 0.44485469, 0.12774117], "xyz": [10.86950779119215, 5.136253570624704, 1.5237148213931984], "properties": {"selective_dynamics": [true, true, true]}, "label": "Se"}], "@version": null}, "@module": "doped.core", "@class": "DefectEntry", "@version": null}} \ No newline at end of file diff --git a/tests/test_analysis.py b/tests/test_analysis.py index cce9c50a..65b709d1 100644 --- a/tests/test_analysis.py +++ b/tests/test_analysis.py @@ -116,21 +116,22 @@ def test_DefectsParser_CdTe(self): for warn in w ) # KPOINTS warning assert any( - f"Warning(s) encountered when parsing Int_Te_3_Unperturbed_1 at " - f"{self.CdTe_EXAMPLE_DIR}/Int_Te_3_Unperturbed_1/vasp_ncl:\nThere are mismatching " - f"INCAR tags for your bulk and defect calculations which are likely to cause severe " - f"errors in the parsed results (energies). Found the following differences:\n(in the " - f"format: (INCAR tag, value in bulk calculation, value in defect calculation)):\n[(" - f"'ADDGRID', True, False)]\nThe same INCAR settings should be used in both " - f"calculations for these tags which can affect energies!" in str(warn.message) + all( + i in str(warn.message) + for i in [ + f"Warning(s) encountered when parsing Int_Te_3_Unperturbed_1 at " + f"{self.CdTe_EXAMPLE_DIR}/Int_Te_3_Unperturbed_1/vasp_ncl:", + "There are mismatching INCAR tags for your bulk and defect calculations", + ] + ) for warn in w ) # INCAR warning assert any( all( i in str(warn.message) for i in [ - f"Warning(s) encountered when parsing Int_Te_3_2 at" - f" {self.CdTe_EXAMPLE_DIR}/Int_Te_3_2/vasp_ncl", + f"Warning(s) encountered when parsing Int_Te_3_2 at " + f"{self.CdTe_EXAMPLE_DIR}/Int_Te_3_2/vasp_ncl", "Multiple `OUTCAR` files found in defect directory", ] )