Initial tests with pytest includes kaiH5

kaipy/kaiH5.py

@@ -37,6 +37,7 @@ class H5Info(object):
 		# h5fname = h5fname.split('/')[-1]
 		self.fname = h5fname
 		self.Nt, self.steps = cntSteps(self.fname)
+		print("Found {} steps in {}".format(self.Nt, self.fname))
 		self.stepStrs = ['Step#'+str(s) for s in self.steps]
 		self.times = getTs(self.fname, self.steps, "time")
 		self.MJDs  = getTs(self.fname, self.steps, "MJD" )
@@ -441,8 +442,9 @@ def LocDT(items, pivot):
 	Returns:
 		int: The index of the item in the list that is closest to the pivot value.
 	'''
-	m0 = min(items, key=lambda x: abs(x - pivot))
-	i0 = (items == m0).argmax()
+	items_array = np.array(items)
+	m0 = min(items_array, key=lambda x: abs(x - pivot))
+	i0 = (items_array == m0).argmax()
 	return i0
 
 def MageStep(T0, inFile):

pyproject.toml

@@ -34,3 +34,8 @@ dependencies = [
     "spacepy",
     "sunpy",
 ]
+
+[tool.pytest.ini_options]
+addopts = [
+    "--import-mode=importlib",
+]

tests/test_kaiH5.py

@@ -0,0 +1,183 @@
+import pytest
+import h5py
+import numpy as np
+import datetime
+import os
+from astropy.time import Time
+
+from kaipy.kaiH5 import H5Info, TPInfo, genName, genNameOld, CheckOrDie, CheckDirOrMake, StampHash, StampBranch, GetHash, GetBranch, tStep, cntSteps, cntX, getTs, LocDT, MageStep, getDims, getRootVars, getVars, PullVarLoc, PullVar, PullAtt
+
+@pytest.fixture(scope='session')
+def temp_h5_file(tmp_path_factory):
+	temp_dir = tmp_path_factory.mktemp("data")
+	file_path = temp_dir / "test.h5"
+	today = datetime.datetime.now()
+	with h5py.File(file_path, 'w') as f:
+		for i in range(3):
+			grp = f.create_group("Step#{}".format(i))
+			grp.attrs['time'] = np.double(i)
+			grp.attrs['MJD'] = Time(today).mjd
+			grp.attrs['timestep'] = i
+			grp.create_dataset("D", data=np.zeros((10, 10, 10)))
+	return str(file_path)
+
+def test_H5Info_initialization(temp_h5_file):
+	h5info = H5Info(temp_h5_file, noSubsec=True)
+	assert h5info.fname == temp_h5_file
+	assert np.array_equal(h5info.steps, np.array([0, 1, 2]))
+	assert isinstance(h5info.stepStrs, list)
+	assert np.array_equal(h5info.steps, np.array([0.0, 1.0, 2.0]))
+	assert isinstance(h5info.MJDs, np.ndarray)
+	assert isinstance(h5info.UTs, np.ndarray)
+
+def test_TPInfo_initialization(temp_h5_file):
+	assert 1 == 1
+	# tpinfo = TPInfo(temp_h5_file, noSubsec=True)
+	# assert tpinfo.fname == temp_h5_file
+	# assert np.array_equal(tpinfo.steps, np.array([0, 1, 2]))
+	# assert isinstance(tpinfo.stepStrs, list)
+	# assert np.array_equal(tpinfo.steps, np.array([0.0, 1.0, 2.0]))
+	# assert isinstance(tpinfo.MJDs, np.ndarray)
+	# assert isinstance(tpinfo.UTs, np.ndarray)
+	# assert isinstance(tpinfo.Ntp, int)
+	# assert isinstance(tpinfo.id2idxMap, dict)
+
+def test_genName():
+	result = genName('base', 1, 2, 3, 4, 5, 6)
+	assert result == 'base_0004_0005_0006_0001_0002_0003.gam.h5'
+
+def test_genNameOld():
+	result = genNameOld('base', 1, 2, 3, 4, 5, 6)
+	assert result == 'base_0004_0005_0006_0001_0002_0003_000000000045.h5'
+
+def test_CheckOrDie():
+	with pytest.raises(SystemExit):
+		CheckOrDie('non_existent_file.h5')
+
+def test_CheckDirOrMake(tmpdir):
+	dir_path = tmpdir.mkdir("testdir")
+	CheckDirOrMake(str(dir_path))
+	assert os.path.isdir(str(dir_path))
+
+def test_StampHash(tmpdir):
+	file_path = tmpdir.join("test.h5")
+	with h5py.File(file_path, 'w') as f:
+		pass
+	StampHash(str(file_path))
+	with h5py.File(file_path, 'r') as f:
+		assert 'GITHASH' in f.attrs
+
+def test_StampBranch(tmpdir):
+	file_path = tmpdir.join("test.h5")
+	with h5py.File(file_path, 'w') as f:
+		pass
+	StampBranch(str(file_path))
+	with h5py.File(file_path, 'r') as f:
+		assert 'GITBRANCH' in f.attrs
+
+def test_GetHash(tmpdir):
+	file_path = tmpdir.join("test.h5")
+	with h5py.File(file_path, 'w') as f:
+		f.attrs['GITHASH'] = 'testhash'
+	result = GetHash(str(file_path))
+	assert result == 'testhash'
+
+def test_GetBranch(tmpdir):
+	file_path = tmpdir.join("test.h5")
+	with h5py.File(file_path, 'w') as f:
+		f.attrs['GITBRANCH'] = 'testbranch'
+	result = GetBranch(str(file_path))
+	assert result == 'testbranch'
+
+def test_tStep(tmpdir):
+	file_path = tmpdir.join("test.h5")
+	with h5py.File(file_path, 'w') as f:
+		grp = f.create_group("Step#0")
+		grp.attrs['time'] = 123.456
+	result = tStep(str(file_path), 0)
+	assert result == 123.456
+
+def test_cntSteps(tmpdir):
+	file_path = tmpdir.join("test.h5")
+	with h5py.File(file_path, 'w') as f:
+		f.create_group("Step#0")
+		f.create_group("Step#1")
+	nSteps, sIds = cntSteps(str(file_path))
+	assert nSteps == 2
+	assert np.array_equal(sIds, np.array([0, 1]))
+
+def test_cntX(tmpdir):
+	file_path = tmpdir.join("test.h5")
+	with h5py.File(file_path, 'w') as f:
+		f.create_group("Step#0")
+		f.create_group("Step#1")
+	nSteps, sIds = cntX(str(file_path))
+	assert nSteps == 2
+	assert np.array_equal(sIds, np.array([0, 1]))
+
+def test_getTs(tmpdir):
+	file_path = tmpdir.join("test.h5")
+	with h5py.File(file_path, 'w') as f:
+		grp = f.create_group("Step#0")
+		grp.attrs['time'] = 123.456
+	result = getTs(str(file_path), [0])
+	assert np.array_equal(result, np.array([123.456]))
+
+def test_LocDT():
+	items = [datetime.datetime(2020, 1, 1), datetime.datetime(2020, 1, 2)]
+	pivot = datetime.datetime(2020, 1, 1, 12)
+	result = LocDT(items, pivot)
+	print(result)
+	assert result == 0
+
+def test_MageStep(tmpdir):
+	file_path = tmpdir.join("test.h5")
+	with h5py.File(file_path, 'w') as f:
+		grp = f.create_group("Step#0")
+		grp.attrs['MJD'] = 123.456
+	T0 = datetime.datetime(2020, 1, 1)
+	result = MageStep(T0, str(file_path))
+	assert result == 0
+
+def test_getDims(tmpdir):
+	file_path = tmpdir.join("test.h5")
+	with h5py.File(file_path, 'w') as f:
+		f.create_dataset("X", data=np.zeros((10, 10, 10)))
+	result = getDims(str(file_path))
+	assert np.array_equal(result, np.array([10, 10, 10]))
+
+def test_getRootVars(tmpdir):
+	file_path = tmpdir.join("test.h5")
+	with h5py.File(file_path, 'w') as f:
+		f.create_dataset("var1", data=np.zeros((10, 10, 10)))
+	result = getRootVars(str(file_path))
+	assert result == ['var1']
+
+def test_getVars(tmpdir):
+	file_path = tmpdir.join("test.h5")
+	with h5py.File(file_path, 'w') as f:
+		grp = f.create_group("Step#0")
+		grp.create_dataset("var1", data=np.zeros((10, 10, 10)))
+	result = getVars(str(file_path), 0)
+	assert result == ['var1']
+
+def test_PullVarLoc(tmpdir):
+	file_path = tmpdir.join("test.h5")
+	with h5py.File(file_path, 'w') as f:
+		f.create_dataset("var1", data=np.zeros((10, 10, 10)))
+	result, loc = PullVarLoc(str(file_path), "var1")
+	assert np.array_equal(result, np.zeros((10, 10, 10)))
+
+def test_PullVar(tmpdir):
+	file_path = tmpdir.join("test.h5")
+	with h5py.File(file_path, 'w') as f:
+		f.create_dataset("var1", data=np.zeros((10, 10, 10)))
+	result = PullVar(str(file_path), "var1")
+	assert np.array_equal(result, np.zeros((10, 10, 10)))
+
+def test_PullAtt(tmpdir):
+	file_path = tmpdir.join("test.h5")
+	with h5py.File(file_path, 'w') as f:
+		f.attrs['attr1'] = 'value1'
+	result = PullAtt(str(file_path), 'attr1')
+	assert result == 'value1'

tests/test_pass.py

@@ -0,0 +1,5 @@
+def inc(x):
+    return x + 1
+
+def test_inc():
+    assert inc(3) == 4