rewriting qe for easier future implementations

setup.py

@@ -8,22 +8,22 @@
     LONG_DESCRIPTION = f.read()
 
 setup(
-    name='aton', 
-    version=__version__,
-    author='Pablo Gila-Herranz',
-    author_email='[email protected]',
-    description=DESCRIPTION,
-    long_description=LONG_DESCRIPTION,
-    long_description_content_type='text/markdown',
-    packages=['aton'],
-    install_requires=['numpy', 'pandas'],
-    extras_requires={
-        'dev': ['pytest', 'twine']
-        },
-    python_requires='>=3',
-    license='AGPL-3.0',
-    keywords=['Aton', 'Neutron', 'Neutron research', 'Spectra', 'Inelastic Neutron Scattering', 'INS', 'Ab-initio', 'DFT', 'Density Functional Theory', 'MD', 'Molecular Dynamics', 'Quantum ESPRESSO', 'Phonopy', 'CASTEP'],
-    classifiers= [
+    name = 'aton', 
+    version = __version__,
+    author = 'Pablo Gila-Herranz',
+    author_email = '[email protected]',
+    description = DESCRIPTION,
+    long_description = LONG_DESCRIPTION,
+    long_description_content_type = 'text/markdown',
+    packages = ['aton'],
+    install_requires = ['numpy', 'pandas', 'scipy', 'matplotlib'],
+    extras_requires = {
+        'dev': ['pytest', 'twine', 'build']
+    },
+    python_requires = '>=3',
+    license = 'AGPL-3.0',
+    keywords = ['Aton', 'Neutron', 'Neutron research', 'Spectra', 'Inelastic Neutron Scattering', 'INS', 'Ab-initio', 'DFT', 'Density Functional Theory', 'MD', 'Molecular Dynamics', 'Quantum ESPRESSO', 'Phonopy', 'CASTEP'],
+    classifiers = [
         "Development Status :: 5 - Production/Stable",
         "Natural Language :: English",
         "Intended Audience :: Science/Research",
@@ -33,3 +33,4 @@
         "Operating System :: Other OS",
     ]
 )
+

tests/test_edit.py

@@ -0,0 +1,105 @@
+from aton.text import edit
+from aton import file
+
+
+folder = 'tests/samples/'
+sample = folder + 'sample.txt'
+sample_copy = folder + 'sample_copy.txt'
+
+
+def test_insert_at():
+    file.copy(sample, sample_copy)
+    edit.insert_at(filepath=sample_copy, text='MIDDLE', position=1)
+    edit.insert_at(filepath=sample_copy, text='START', position=0)
+    edit.insert_at(filepath=sample_copy, text='END', position=-1)
+    with open(sample_copy, 'r') as f:
+        assert f.read() == 'START\nline1\nMIDDLE\nline2\nline3\nline4\nline5\nline6\nline7\nline8\nline9\nEND'
+    file.remove(sample_copy)
+
+
+def test_insert_under():
+    file.copy(sample, sample_copy)
+    edit.insert_under(filepath=sample_copy, key='5', text='!!!', skips=0)
+    with open(sample_copy, 'r') as f:
+        assert f.read() == 'line1\nline2\nline3\nline4\nline5\n!!!\nline6\nline7\nline8\nline9'
+    file.copy(sample, sample_copy)
+    edit.insert_under(filepath=sample_copy, key='5', text='!!!', skips=-1)
+    with open(sample_copy, 'r') as f:
+        assert f.read() == 'line1\nline2\nline3\nline4\n!!!\nline5\nline6\nline7\nline8\nline9'
+    file.copy(sample, sample_copy)
+    edit.insert_under(filepath=sample_copy, key=r'l[a-z]*5', text='!!!', regex=True)
+    with open(sample_copy, 'r') as f:
+        assert f.read() == 'line1\nline2\nline3\nline4\nline5\n!!!\nline6\nline7\nline8\nline9'
+    file.remove(sample_copy)
+
+
+def test_replace():
+    file.copy(sample, sample_copy)
+    edit.replace(filepath=sample_copy, key='line5', text='!!!')
+    with open(sample_copy, 'r') as f:
+        assert f.read() == 'line1\nline2\nline3\nline4\n!!!\nline6\nline7\nline8\nline9'
+    file.remove(sample_copy)
+
+
+def test_replace_line():
+    file.copy(sample, sample_copy)
+    edit.replace_line(filepath=sample_copy, key='line5', text='!!!')
+    with open(sample_copy, 'r') as f:
+        assert f.read() == 'line1\nline2\nline3\nline4\n!!!\nline6\nline7\nline8\nline9'
+    file.copy(sample, sample_copy)
+    edit.replace_line(filepath=sample_copy, key='line5', text='')
+    with open(sample_copy, 'r') as f:
+        assert f.read() == 'line1\nline2\nline3\nline4\nline6\nline7\nline8\nline9'
+    file.remove(sample_copy)
+
+
+def test_replace_between():
+    file.copy(sample, sample_copy)
+    edit.replace_between(filepath=sample_copy, key1='line4', key2='line7', text='!!!')
+    with open(sample_copy, 'r') as f:
+        assert f.read() == 'line1\nline2\nline3\nline4\n!!!\nline7\nline8\nline9'
+    file.remove(sample_copy)
+
+
+def test_remove_between():
+    file.copy(sample, sample_copy)
+    edit.replace_between(filepath=sample_copy, key1='line4', key2='line7', text='')
+    with open(sample_copy, 'r') as f:
+        assert f.read() == 'line1\nline2\nline3\nline4\nline7\nline8\nline9'
+    file.remove(sample_copy)
+
+
+def test_delete_under():
+    file.copy(sample, sample_copy)
+    edit.delete_under(filepath=sample_copy, key='5')
+    with open(sample_copy, 'r') as f:
+        assert f.read() == 'line1\nline2\nline3\nline4\nline5'
+    file.remove(sample_copy)
+
+
+def test_correct_with_dict():
+    correct = {'line1': 'text', 'line5': ''}
+    file.copy(sample, sample_copy)
+    edit.correct_with_dict(filepath=sample_copy, correct=correct)
+    with open(sample_copy, 'r') as f:
+        assert f.read() == 'text\nline2\nline3\nline4\n\nline6\nline7\nline8\nline9'
+    file.remove(sample_copy)
+
+
+def test_template():
+    try:
+        file.remove(sample_copy)
+    except:
+        pass
+    try:
+        edit.from_template(old=sample, new=sample_copy, correct={'line':''}, comment='!!!')
+        with open(sample_copy, 'r') as f:
+            content = f.read()
+            assert content == '!!!\n1\n2\n3\n4\n5\n6\n7\n8\n9'
+    except:
+        assert False
+    try:
+        file.remove(sample_copy)
+    except:
+        pass
+

tests/test_extract.py

@@ -1,32 +1,32 @@
-import thotpy as th
+from aton.text import extract
 
 
 def test_extract_number():
-    assert th.extract.number(' test = 123 number ', 'test') == 123.0
-    assert th.extract.number(' test 123 number ', 'test') == 123.0
+    assert extract.number(' test = 123 number ', 'test') == 123.0
+    assert extract.number(' test 123 number ', 'test') == 123.0
 
 
 def test_extract_string():
-    assert th.extract.string(text=' test = "hello" stop ', name='test', stop='stop', strip=True) == 'hello'
-    assert th.extract.string(text=' test "hello" stop ', name='test', stop='stop', strip=True) == 'hello'
-    assert th.extract.string(text=" test 'hello' stop ", name='test', stop='stop', strip=True) == 'hello'
-    assert th.extract.string(text=" test 'hello' stop ", name='test', stop='stop', strip=False) == "'hello'"
+    assert extract.string(text=' test = "hello" stop ', name='test', stop='stop', strip=True) == 'hello'
+    assert extract.string(text=' test "hello" stop ', name='test', stop='stop', strip=True) == 'hello'
+    assert extract.string(text=" test 'hello' stop ", name='test', stop='stop', strip=True) == 'hello'
+    assert extract.string(text=" test 'hello' stop ", name='test', stop='stop', strip=False) == "'hello'"
 
 
 def test_extract_column():
-    assert th.extract.column(' 123 456.5 789  ', 2) == 789
+    assert extract.column(' 123 456.5 789  ', 2) == 789
 
 
 def test_extract_coords():
-    assert th.extract.coords('coordinates: 1.0, 2.0 and 3 these were the coordinates') ==[1.0, 2.0, 3.0]
+    assert extract.coords('coordinates: 1.0, 2.0 and 3 these were the coordinates') ==[1.0, 2.0, 3.0]
 
 
 def test_extract_element():
     string = '  element I Lead Pb Nitrogen H2, Xx2 fake element, O Oxygen, He4 isotope Ag Element '
-    assert th.extract.element(text=string, index=0) == 'I'
-    assert th.extract.element(text=string, index=1) == 'Pb'
-    assert th.extract.element(text=string, index=2) == 'H2'
-    assert th.extract.element(text=string, index=3) == 'O'
-    assert th.extract.element(text=string, index=4) == 'He4'
-    assert th.extract.element(text=string, index=5) == 'Ag'
+    assert extract.element(text=string, index=0) == 'I'
+    assert extract.element(text=string, index=1) == 'Pb'
+    assert extract.element(text=string, index=2) == 'H2'
+    assert extract.element(text=string, index=3) == 'O'
+    assert extract.element(text=string, index=4) == 'He4'
+    assert extract.element(text=string, index=5) == 'Ag'
 

tests/test_file.py

@@ -1,6 +1,4 @@
-'''For this path to be detected properly, the `pytest` must be executed from `ThotPy`!'''
-
-import thotpy as th
+from aton import file
 
 
 folder = 'tests/samples/'
@@ -14,118 +12,100 @@
 def test_get():
     # Clean from previous tests
     try:
-        th.file.remove(sample_copy)
+        file.remove(sample_copy)
     except:
         pass
     # Finds an existing file
     try:
-        assert th.file.get(sample) != None
+        assert file.get(sample) != None
         assert True
     except FileNotFoundError:
         assert False
     # Does not find a non-existing file
     try:
-        th.file.get(sample_copy)
+        file.get(sample_copy)
         assert False
     except FileNotFoundError:
         assert True
     # get_list, 'tests/sample.txt' in 'fullpath/tests/sample.txt'
     try:
-        assert sample in th.file.get_list(folder, filters='sample')[0]
-    except:
-        assert False
-
-
-def test_template():
-    try:
-        th.file.remove(sample_copy)
-    except:
-        pass
-    try:
-        th.file.from_template(old=sample, new=sample_copy, replaces={'line':''}, comment='!!!')
-        with open(sample_copy, 'r') as f:
-            content = f.read()
-            assert content == '!!!\n1\n2\n3\n4\n5\n6\n7\n8\n9'
+        assert sample in file.get_list(folder, filters='sample')[0]
     except:
         assert False
-    try:
-        th.file.remove(sample_copy)
-    except:
-        pass
 
 
 def test_copy():
     try:
-        th.file.remove(sample_copy)
-        th.file.remove(sample_copy_2)
+        file.remove(sample_copy)
+        file.remove(sample_copy_2)
     except:
         pass
     # Copy files
     try:
-        th.file.copy(sample, sample_copy)
-        assert th.file.get(sample_copy) != None
+        file.copy(sample, sample_copy)
+        assert file.get(sample_copy) != None
     except FileNotFoundError:
         assert False
     # Move files
     try:
-        th.file.move(sample_copy, sample_copy_2)
-        assert th.file.get(sample_copy_2) != None
+        file.move(sample_copy, sample_copy_2)
+        assert file.get(sample_copy_2) != None
     except:
         assert False
     try:
-        th.file.get(sample_copy)
+        file.get(sample_copy)
         assert False
     except FileNotFoundError:
         assert True
     # Remove
     try:
-        th.file.remove(sample_copy_2)
+        file.remove(sample_copy_2)
     except:
         assert False
     try:
-        th.file.get(sample_copy_2)
+        file.get(sample_copy_2)
         assert False
     except:
         assert True
 
 
 def test_rename():
     try:
-        th.file.remove(sample_copy)
-        th.file.remove(sample_ok)
+        file.remove(sample_copy)
+        file.remove(sample_ok)
     except:
         pass
-    th.file.copy(sample, sample_copy)
-    th.file.rename_on_folder(old='copy', new='ok', folder=folder)
+    file.copy(sample, sample_copy)
+    file.rename_on_folder(old='copy', new='ok', folder=folder)
     try:
-        th.file.remove(sample_ok)
+        file.remove(sample_ok)
         assert True
     except:
         assert False
     try:
-        th.file.remove(sample_copy)
+        file.remove(sample_copy)
         assert False
     except:
         assert True
 
 
 def test_folders():
     try:
-        th.file.remove(sample_copy)
-        th.file.remove(sample_copy_2)
-        th.file.remove(sample_ok)
-        th.file.remove(sample_ok_2)
+        file.remove(sample_copy)
+        file.remove(sample_copy_2)
+        file.remove(sample_ok)
+        file.remove(sample_ok_2)
     except:
         pass
-    th.file.copy_to_folders(extension='.txt', strings_to_delete=['.txt'], folder=folder)
+    file.copy_to_folders(extension='.txt', strings_to_delete=['.txt'], folder=folder)
     try:
-        assert th.file.get_list(folder=folder+'sample', abspath=False) == ['sample.txt']
+        assert file.get_list(folder=folder+'sample', abspath=False) == ['sample.txt']
     except:
         assert False
     # Check that the folder is deleted
-    th.file.remove(folder+'sample')
+    file.remove(folder+'sample')
     try:
-        th.file.get_list(folder+'sample')
+        file.get_list(folder+'sample')
         assert False
     except FileNotFoundError:
         assert True

tests/test_find.py

@@ -1,8 +1,7 @@
-from thotpy import find
+from aton.text import find
 
 
 sample = 'tests/samples/sample.txt'
-'''For this path to be detected properly, the `pytest` must be executed from `ThotPy`!'''
 
 
 def test_lines():