From 971c08685080b6a7146b6de077d721d05d39c778 Mon Sep 17 00:00:00 2001 From: Guillaume Lemaitre Date: Fri, 21 Jul 2017 18:18:12 +0200 Subject: [PATCH 1/2] CI move to pytest --- .travis.yml | 7 +- tests/__init__.py | 0 {test_data => tests/data}/4d_map.spc | Bin .../data}/BC408_5mmHorizontal.spc | Bin .../data}/CAthickyellow_try4_17_ZSCAN.spc | Bin .../data}/CAthickyellow_try4_18.spc | Bin {test_data => tests/data}/DERt3_1.spc | Bin {test_data => tests/data}/DOERNER.spc | Bin {test_data => tests/data}/Ft-ir.spc | Bin {test_data => tests/data}/HENE25.SPC | Bin {test_data => tests/data}/HENE27.SPC | Bin {test_data => tests/data}/KRY3.SPC | Bin {test_data => tests/data}/KRY4.SPC | Bin {test_data => tests/data}/KRY5.SPC | Bin {test_data => tests/data}/MERC.SPC | Bin {test_data => tests/data}/NMR_FID.SPC | Bin {test_data => tests/data}/NMR_SPC.SPC | Bin {test_data => tests/data}/RAMAN.SPC | Bin {test_data => tests/data}/RUBY18.SPC | Bin {test_data => tests/data}/TS01.SPC | Bin 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=> tests/data}/txt3/TS01.SPC.txt (100%) create mode 100644 tests/data/txt3/__init__.py rename {test_data => tests/data}/txt3/kry2.spc.txt (100%) rename {test_data => tests/data}/txt3/m_evenz.spc.txt (100%) rename {test_data => tests/data}/txt3/m_ordz.spc.txt (100%) rename {test_data => tests/data}/txt3/m_xyxy.spc.txt (100%) rename {test_data => tests/data}/txt3/ms.spc.txt (100%) rename {test_data => tests/data}/txt3/nir.spc.txt (100%) rename {test_data => tests/data}/txt3/s_evenx.spc.txt (100%) rename {test_data => tests/data}/txt3/s_xy.spc.txt (100%) create mode 100644 tests/test_spc.py diff --git a/.travis.yml b/.travis.yml index 3c7b10f..a8d687d 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,13 +1,10 @@ language: python python: - "2.7" - - "3.2" - - "3.3" - "3.4" - "3.5" - - "3.5-dev" # 3.5 development branch - - "nightly" # currently points to 3.6-dev + - "3.6" # command to install dependencies install: "pip install -r requirements.txt" # command to run tests -script: ./test.py +script: py.test tests diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/test_data/4d_map.spc b/tests/data/4d_map.spc similarity index 100% rename from test_data/4d_map.spc rename to tests/data/4d_map.spc diff --git a/test_data/BC408_5mmHorizontal.spc b/tests/data/BC408_5mmHorizontal.spc similarity index 100% rename from test_data/BC408_5mmHorizontal.spc rename to tests/data/BC408_5mmHorizontal.spc diff --git a/test_data/CAthickyellow_try4_17_ZSCAN.spc b/tests/data/CAthickyellow_try4_17_ZSCAN.spc similarity index 100% rename from test_data/CAthickyellow_try4_17_ZSCAN.spc rename to tests/data/CAthickyellow_try4_17_ZSCAN.spc diff --git a/test_data/CAthickyellow_try4_18.spc b/tests/data/CAthickyellow_try4_18.spc similarity index 100% rename from test_data/CAthickyellow_try4_18.spc rename to tests/data/CAthickyellow_try4_18.spc diff --git a/test_data/DERt3_1.spc b/tests/data/DERt3_1.spc similarity index 100% rename from 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index 0000000..e69de29 diff --git a/test_data/txt/kry2.spc.txt b/tests/data/txt/kry2.spc.txt similarity index 100% rename from test_data/txt/kry2.spc.txt rename to tests/data/txt/kry2.spc.txt diff --git a/test_data/txt/m_evenz.spc.txt b/tests/data/txt/m_evenz.spc.txt similarity index 100% rename from test_data/txt/m_evenz.spc.txt rename to tests/data/txt/m_evenz.spc.txt diff --git a/test_data/txt/m_ordz.spc.txt b/tests/data/txt/m_ordz.spc.txt similarity index 100% rename from test_data/txt/m_ordz.spc.txt rename to tests/data/txt/m_ordz.spc.txt diff --git a/test_data/txt/m_xyxy.spc.txt b/tests/data/txt/m_xyxy.spc.txt similarity index 100% rename from test_data/txt/m_xyxy.spc.txt rename to tests/data/txt/m_xyxy.spc.txt diff --git a/test_data/txt/ms.spc.txt b/tests/data/txt/ms.spc.txt similarity index 100% rename from test_data/txt/ms.spc.txt rename to tests/data/txt/ms.spc.txt diff --git a/test_data/txt/nir.spc.txt b/tests/data/txt/nir.spc.txt similarity index 100% rename from test_data/txt/nir.spc.txt rename to tests/data/txt/nir.spc.txt diff --git a/test_data/txt/s_evenx.spc.txt b/tests/data/txt/s_evenx.spc.txt similarity index 100% rename from test_data/txt/s_evenx.spc.txt rename to tests/data/txt/s_evenx.spc.txt diff --git a/test_data/txt/s_xy.spc.txt b/tests/data/txt/s_xy.spc.txt similarity index 100% rename from test_data/txt/s_xy.spc.txt rename to tests/data/txt/s_xy.spc.txt diff --git a/test_data/txt2/4d_map.spc.txt b/tests/data/txt2/4d_map.spc.txt similarity index 100% rename from test_data/txt2/4d_map.spc.txt rename to tests/data/txt2/4d_map.spc.txt diff --git a/test_data/txt2/BC408_5mmHorizontal.spc.txt b/tests/data/txt2/BC408_5mmHorizontal.spc.txt similarity index 100% rename from test_data/txt2/BC408_5mmHorizontal.spc.txt rename to tests/data/txt2/BC408_5mmHorizontal.spc.txt diff --git a/test_data/txt2/CAthickyellow_try4_17_ZSCAN.spc.txt b/tests/data/txt2/CAthickyellow_try4_17_ZSCAN.spc.txt similarity index 100% rename from test_data/txt2/CAthickyellow_try4_17_ZSCAN.spc.txt rename to tests/data/txt2/CAthickyellow_try4_17_ZSCAN.spc.txt diff --git a/test_data/txt2/CAthickyellow_try4_18.spc.txt b/tests/data/txt2/CAthickyellow_try4_18.spc.txt similarity index 100% rename from test_data/txt2/CAthickyellow_try4_18.spc.txt rename to tests/data/txt2/CAthickyellow_try4_18.spc.txt diff --git a/test_data/txt2/DERt3_1.spc.txt b/tests/data/txt2/DERt3_1.spc.txt similarity index 100% rename from test_data/txt2/DERt3_1.spc.txt rename to tests/data/txt2/DERt3_1.spc.txt diff --git a/test_data/txt2/DOERNER.spc.txt b/tests/data/txt2/DOERNER.spc.txt similarity index 100% rename from test_data/txt2/DOERNER.spc.txt rename to tests/data/txt2/DOERNER.spc.txt diff --git a/test_data/txt2/Ft-ir.spc.txt b/tests/data/txt2/Ft-ir.spc.txt similarity index 100% rename from test_data/txt2/Ft-ir.spc.txt rename to tests/data/txt2/Ft-ir.spc.txt diff --git a/test_data/txt2/HENE25.SPC.txt b/tests/data/txt2/HENE25.SPC.txt similarity index 100% rename from test_data/txt2/HENE25.SPC.txt rename to tests/data/txt2/HENE25.SPC.txt diff --git a/test_data/txt2/HENE27.SPC.txt b/tests/data/txt2/HENE27.SPC.txt similarity index 100% rename from test_data/txt2/HENE27.SPC.txt rename to tests/data/txt2/HENE27.SPC.txt diff --git a/test_data/txt2/KRY3.SPC.txt b/tests/data/txt2/KRY3.SPC.txt similarity index 100% rename from test_data/txt2/KRY3.SPC.txt rename to tests/data/txt2/KRY3.SPC.txt diff --git a/test_data/txt2/KRY4.SPC.txt b/tests/data/txt2/KRY4.SPC.txt similarity index 100% rename from test_data/txt2/KRY4.SPC.txt rename to tests/data/txt2/KRY4.SPC.txt diff --git a/test_data/txt2/KRY5.SPC.txt b/tests/data/txt2/KRY5.SPC.txt similarity index 100% rename from test_data/txt2/KRY5.SPC.txt rename to tests/data/txt2/KRY5.SPC.txt diff --git a/test_data/txt2/MERC.SPC.txt b/tests/data/txt2/MERC.SPC.txt similarity index 100% rename from test_data/txt2/MERC.SPC.txt rename to tests/data/txt2/MERC.SPC.txt diff --git a/test_data/txt2/NMR_FID.SPC.txt b/tests/data/txt2/NMR_FID.SPC.txt similarity index 100% rename from test_data/txt2/NMR_FID.SPC.txt rename to tests/data/txt2/NMR_FID.SPC.txt diff --git a/test_data/txt2/NMR_SPC.SPC.txt b/tests/data/txt2/NMR_SPC.SPC.txt similarity index 100% rename from test_data/txt2/NMR_SPC.SPC.txt rename to tests/data/txt2/NMR_SPC.SPC.txt diff --git a/test_data/txt2/RAMAN.SPC.txt b/tests/data/txt2/RAMAN.SPC.txt similarity index 100% rename from test_data/txt2/RAMAN.SPC.txt rename to tests/data/txt2/RAMAN.SPC.txt diff --git a/test_data/txt2/RUBY18.SPC.txt b/tests/data/txt2/RUBY18.SPC.txt similarity index 100% rename from test_data/txt2/RUBY18.SPC.txt rename to tests/data/txt2/RUBY18.SPC.txt diff --git a/test_data/txt2/TS01.SPC.txt b/tests/data/txt2/TS01.SPC.txt similarity index 100% rename from test_data/txt2/TS01.SPC.txt rename to tests/data/txt2/TS01.SPC.txt diff --git a/tests/data/txt2/__init__.py b/tests/data/txt2/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/test_data/txt2/kry2.spc.txt b/tests/data/txt2/kry2.spc.txt similarity index 100% rename from test_data/txt2/kry2.spc.txt rename to tests/data/txt2/kry2.spc.txt diff --git a/test_data/txt2/m_evenz.spc.txt b/tests/data/txt2/m_evenz.spc.txt similarity index 100% rename from test_data/txt2/m_evenz.spc.txt rename to tests/data/txt2/m_evenz.spc.txt diff --git a/test_data/txt2/m_ordz.spc.txt b/tests/data/txt2/m_ordz.spc.txt similarity index 100% rename from test_data/txt2/m_ordz.spc.txt rename to tests/data/txt2/m_ordz.spc.txt diff --git a/test_data/txt2/m_xyxy.spc.txt b/tests/data/txt2/m_xyxy.spc.txt similarity index 100% rename from test_data/txt2/m_xyxy.spc.txt rename to tests/data/txt2/m_xyxy.spc.txt diff --git a/test_data/txt2/ms.spc.txt b/tests/data/txt2/ms.spc.txt similarity index 100% rename from test_data/txt2/ms.spc.txt rename to tests/data/txt2/ms.spc.txt diff --git a/test_data/txt2/nir.spc.txt b/tests/data/txt2/nir.spc.txt similarity index 100% rename from test_data/txt2/nir.spc.txt rename to tests/data/txt2/nir.spc.txt diff --git a/test_data/txt2/s_evenx.spc.txt b/tests/data/txt2/s_evenx.spc.txt similarity index 100% rename from test_data/txt2/s_evenx.spc.txt rename to tests/data/txt2/s_evenx.spc.txt diff --git a/test_data/txt2/s_xy.spc.txt b/tests/data/txt2/s_xy.spc.txt similarity index 100% rename from test_data/txt2/s_xy.spc.txt rename to tests/data/txt2/s_xy.spc.txt diff --git a/test_data/txt2/test_input.spc.txt b/tests/data/txt2/test_input.spc.txt similarity index 100% rename from test_data/txt2/test_input.spc.txt rename to tests/data/txt2/test_input.spc.txt diff --git a/test_data/txt3/4d_map.spc.txt b/tests/data/txt3/4d_map.spc.txt similarity index 100% rename from test_data/txt3/4d_map.spc.txt rename to tests/data/txt3/4d_map.spc.txt diff --git a/test_data/txt3/BC408_5mmHorizontal.spc.txt b/tests/data/txt3/BC408_5mmHorizontal.spc.txt similarity index 100% rename from test_data/txt3/BC408_5mmHorizontal.spc.txt rename to tests/data/txt3/BC408_5mmHorizontal.spc.txt diff --git a/test_data/txt3/CAthickyellow_try4_17_ZSCAN.spc.txt b/tests/data/txt3/CAthickyellow_try4_17_ZSCAN.spc.txt similarity index 100% rename from test_data/txt3/CAthickyellow_try4_17_ZSCAN.spc.txt rename to tests/data/txt3/CAthickyellow_try4_17_ZSCAN.spc.txt diff --git a/test_data/txt3/CAthickyellow_try4_18.spc.txt b/tests/data/txt3/CAthickyellow_try4_18.spc.txt similarity index 100% rename from test_data/txt3/CAthickyellow_try4_18.spc.txt rename to tests/data/txt3/CAthickyellow_try4_18.spc.txt diff --git a/test_data/txt3/DERt3_1.spc.txt b/tests/data/txt3/DERt3_1.spc.txt similarity index 100% rename from test_data/txt3/DERt3_1.spc.txt rename to tests/data/txt3/DERt3_1.spc.txt diff --git a/test_data/txt3/DOERNER.spc.txt b/tests/data/txt3/DOERNER.spc.txt similarity index 100% rename from test_data/txt3/DOERNER.spc.txt rename to tests/data/txt3/DOERNER.spc.txt diff --git a/test_data/txt3/Ft-ir.spc.txt b/tests/data/txt3/Ft-ir.spc.txt similarity index 100% rename from test_data/txt3/Ft-ir.spc.txt rename to tests/data/txt3/Ft-ir.spc.txt diff --git a/test_data/txt3/HENE25.SPC.txt b/tests/data/txt3/HENE25.SPC.txt similarity index 100% rename from test_data/txt3/HENE25.SPC.txt rename to tests/data/txt3/HENE25.SPC.txt diff --git a/test_data/txt3/HENE27.SPC.txt b/tests/data/txt3/HENE27.SPC.txt similarity index 100% rename from test_data/txt3/HENE27.SPC.txt rename to tests/data/txt3/HENE27.SPC.txt diff --git a/test_data/txt3/KRY3.SPC.txt b/tests/data/txt3/KRY3.SPC.txt similarity index 100% rename from test_data/txt3/KRY3.SPC.txt rename to tests/data/txt3/KRY3.SPC.txt diff --git a/test_data/txt3/KRY4.SPC.txt b/tests/data/txt3/KRY4.SPC.txt similarity index 100% rename from test_data/txt3/KRY4.SPC.txt rename to tests/data/txt3/KRY4.SPC.txt diff --git a/test_data/txt3/KRY5.SPC.txt b/tests/data/txt3/KRY5.SPC.txt similarity index 100% rename from test_data/txt3/KRY5.SPC.txt rename to tests/data/txt3/KRY5.SPC.txt diff --git a/test_data/txt3/MERC.SPC.txt b/tests/data/txt3/MERC.SPC.txt similarity index 100% rename from test_data/txt3/MERC.SPC.txt rename to tests/data/txt3/MERC.SPC.txt diff --git a/test_data/txt3/NMR_FID.SPC.txt b/tests/data/txt3/NMR_FID.SPC.txt similarity index 100% rename from test_data/txt3/NMR_FID.SPC.txt rename to tests/data/txt3/NMR_FID.SPC.txt diff --git a/test_data/txt3/NMR_SPC.SPC.txt b/tests/data/txt3/NMR_SPC.SPC.txt similarity index 100% rename from test_data/txt3/NMR_SPC.SPC.txt rename to tests/data/txt3/NMR_SPC.SPC.txt diff --git a/test_data/txt3/RAMAN.SPC.txt b/tests/data/txt3/RAMAN.SPC.txt similarity index 100% rename from test_data/txt3/RAMAN.SPC.txt rename to tests/data/txt3/RAMAN.SPC.txt diff --git a/test_data/txt3/RUBY18.SPC.txt b/tests/data/txt3/RUBY18.SPC.txt similarity index 100% rename from test_data/txt3/RUBY18.SPC.txt rename to tests/data/txt3/RUBY18.SPC.txt diff --git a/test_data/txt3/TS01.SPC.txt b/tests/data/txt3/TS01.SPC.txt similarity index 100% rename from test_data/txt3/TS01.SPC.txt rename to tests/data/txt3/TS01.SPC.txt diff --git a/tests/data/txt3/__init__.py b/tests/data/txt3/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/test_data/txt3/kry2.spc.txt b/tests/data/txt3/kry2.spc.txt similarity index 100% rename from test_data/txt3/kry2.spc.txt rename to tests/data/txt3/kry2.spc.txt diff --git a/test_data/txt3/m_evenz.spc.txt b/tests/data/txt3/m_evenz.spc.txt similarity index 100% rename from test_data/txt3/m_evenz.spc.txt rename to tests/data/txt3/m_evenz.spc.txt diff --git a/test_data/txt3/m_ordz.spc.txt b/tests/data/txt3/m_ordz.spc.txt similarity index 100% rename from test_data/txt3/m_ordz.spc.txt rename to tests/data/txt3/m_ordz.spc.txt diff --git a/test_data/txt3/m_xyxy.spc.txt b/tests/data/txt3/m_xyxy.spc.txt similarity index 100% rename from test_data/txt3/m_xyxy.spc.txt rename to tests/data/txt3/m_xyxy.spc.txt diff --git a/test_data/txt3/ms.spc.txt b/tests/data/txt3/ms.spc.txt similarity index 100% rename from test_data/txt3/ms.spc.txt rename to tests/data/txt3/ms.spc.txt diff --git a/test_data/txt3/nir.spc.txt b/tests/data/txt3/nir.spc.txt similarity index 100% rename from test_data/txt3/nir.spc.txt rename to tests/data/txt3/nir.spc.txt diff --git a/test_data/txt3/s_evenx.spc.txt b/tests/data/txt3/s_evenx.spc.txt similarity index 100% rename from test_data/txt3/s_evenx.spc.txt rename to tests/data/txt3/s_evenx.spc.txt diff --git a/test_data/txt3/s_xy.spc.txt b/tests/data/txt3/s_xy.spc.txt similarity index 100% rename from test_data/txt3/s_xy.spc.txt rename to tests/data/txt3/s_xy.spc.txt diff --git a/tests/test_spc.py b/tests/test_spc.py new file mode 100644 index 0000000..8f76bf1 --- /dev/null +++ b/tests/test_spc.py @@ -0,0 +1,108 @@ +import os +from os.path import join, dirname + +import numpy as np +import pandas as pd +from numpy.testing import assert_allclose + +import spc + + +def _list_all_spc_files(): + """List the spc files in the data folders.""" + path_data = join(dirname(__file__), 'data') + filenames = [filename + for filename in os.listdir(path_data) + if filename.lower().endswith('spc')] + return filenames + + +def _split_data(spc_file): + """Reorganize into numpy format the data depending of the format. + + Parameters + ---------- + spc_file : spc.File + The spc.File object to be reorganized to ease the testing. + + Returns + ------- + X : ndarray, shape (n_spectra, n_frequency) or (n_frequency,) + The x axis. + + Y : ndarray shape (n_spectra, n_frequency) + The y axis. + + """ + if (spc_file.dat_fmt == 'gx-y' or + spc_file.dat_fmt == 'x-y'): + X = spc_file.x + elif spc_file.dat_fmt == '-xy': + X = np.array([f.x for f in spc_file.sub]) + Y = np.array([f.y for f in spc_file.sub]) + + return X, Y + + +def _read_expected_file(spc_filename, spc_file_format): + """Reorganize into numpy format the data depending of the format. + + Parameters + ---------- + spc_filename : str + The filename of the SPC file which will be checked. + + spc_file_format : str + The format of the SPC file: '-xy', 'x-y', or 'gx-y'. + + Returns + ------- + X : ndarray, shape (n_spectra, n_frequency) or (n_frequency,) + The x axis. + + Y : ndarray shape (n_spectra, n_frequency) + The y axis. + + """ + path_data = join(dirname(__file__), 'data', 'txt2') + data_expected = pd.read_csv(join(path_data, spc_filename + '.txt'), + sep='\t', header=None, skip_blank_lines=False) + if (spc_file_format == 'gx-y' or + spc_file_format == 'x-y'): + X = data_expected.iloc[:, 0].values.T + Y = data_expected.iloc[:, 1:].values.T + elif spc_file_format == '-xy': + data_expected['group_no'] = data_expected.isnull().all(axis=1).cumsum() + # split into a list of DataFrames + data_expected = [ + (data_expected.loc[data_expected['group_no'] == i, + [0, 1]]).dropna() + for i in range(data_expected['group_no'].iloc[-1])] + X, Y = [], [] + for df in data_expected: + X.append(df.iloc[:, 0].values.T) + Y.append(df.iloc[:, 1].values.T) + X = np.array(X) + Y = np.array(Y) + + return X, Y + + +def test_spc(): + filenames_spc = _list_all_spc_files() + + for filename in filenames_spc: + path_data = join(dirname(__file__), 'data') + file_spc = spc.File(join(path_data, filename)) + X, Y = _split_data(file_spc) + X_expected, Y_expected = _read_expected_file(filename, + file_spc.dat_fmt) + if file_spc.dat_fmt == '-xy': + for x, y, x_expected, y_expected in zip(X, Y, + X_expected, + Y_expected): + assert_allclose(x, x_expected) + assert_allclose(y, y_expected) + else: + assert_allclose(X, X_expected) + assert_allclose(Y, Y_expected) From 390e462b8bad5dfb9ee473e5c30f3c3fb8fd4917 Mon Sep 17 00:00:00 2001 From: Guillaume Lemaitre Date: Fri, 21 Jul 2017 18:28:00 +0200 Subject: [PATCH 2/2] install dependency for testign --- .travis.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index a8d687d..da1afa8 100644 --- a/.travis.yml +++ b/.travis.yml @@ -5,6 +5,8 @@ python: - "3.5" - "3.6" # command to install dependencies -install: "pip install -r requirements.txt" +install: + - pip install -r requirements.txt + - pip install pytest pytest-cov pandas # command to run tests -script: py.test tests +script: py.test --cov=spc tests