Restructure, Reduce Test Time, Migrate MELTS to Draft

test/util/test_util_melts.py → draft/test_util_melts.py

@@ -1,7 +1,7 @@
 import unittest
 from pathlib import Path
 from collections import OrderedDict
-from pyrolite.util.melts import *
+from .melts import *
 from pyrolite.data.melts.env import MELTS_environment_variables
 from pyrolite.util.general import remove_tempdir, internet_connection, \
                                   check_perl, temp_path

pyrolite/data/georoc/GEOROC_CFB_Dataset_List.csv

@@ -0,0 +1,42 @@
+AUSTRALIA.csv
+AVANAVERA LARGE IGNEOUS PROVINCE.csv
+CENTRAL ATLANTIC MAGMATIC PROVINCE - CAMP.csv
+CHILCOTIN PLATEAU BASALTS.csv
+COMEI LARGE IGNEOUS PROVINCE.csv
+DECCAN.csv
+EMEISHAN.csv
+ETENDEKA PROVINCE.csv
+ETHIOPIAN PLATEAU.csv
+FRANKLIN LARGE IGNEOUS PROVINCE.csv
+GUNBARREL IGNEOUS EVENT.csv
+HIGH ARCTIC LARGE IGNEOUS PROVINCE.csv
+KAROO AND FERRAR PROVINCES.csv
+KUONAMKA LARGE IGNEOUS PROVINCE.csv
+KUZNETSK BASIN OR KUZBASS TRAPS.csv
+LAKE VICTORIA LARGE IGNEOUS PROVINCE.csv
+MACKENZIE LARGE IGNEOUS PROVINCE.csv
+MADAGASCAR FLOOD BASALT.csv
+MAIMECHA-KOTUI PROVINCE.csv
+MALANI MAGMATIC PROVINCE;INDIA.csv
+MARATHON LARGE IGNEOUS PROVINCE.csv
+MARNDA MOORN LARGE IGNEOUS PROVINCE.csv
+MATACHEWAN LARGE IGNEOUS PROVINCE.csv
+MIDCONTINENT RIFT SYSTEM - KEWEENAWAN.csv
+NANDALING - YANSHAN BELT.csv
+NILUFER UNIT - YENISEHIR ASSOCIATION - PONTIDES.csv
+NORTH ATLANTIC IGNEOUS PROVINCE OR NAIP.csv
+NORTH GREENLAND  PROTEROZOIC.csv
+PANJAL-SOUTH QIANGTANG LARGE IGNEOUS PROVINCE.csv
+PARANA.csv
+QIANGTANG FLOOD BASALT PROVINCE.csv
+RAJAHMUNDRY TRAPS.csv
+RAJMAHAL-BENGAL-SYLHET.csv
+RAMPUR-GARHWAL-MANDI-DARLA PROVINCE.csv
+SIBERIAN TRAPS.csv
+SOUTH TETHYAN SUTURE ZONE - PAKISTAN.csv
+TARIM LARGE IGNEOUS PROVINCE.csv
+TIBESTI VOLCANIC PROVINCE.csv
+UMKONDO LARGE IGNEOUS PROVINCE.csv
+WRANGELLIA.csv
+YELLOWSTONE-SNAKE RIVER PLAIN VOLCANIC PROVINCE.csv
+YEMEN PLATEAU.csv

pyrolite/data/georoc/GEOROC_Convergent_Dataset_List.csv

@@ -0,0 +1,42 @@
+AEGEAN ARC.csv
+AEOLIAN ARC.csv
+ALEUTIAN ARC.csv
+ANDEAN ARC part1.csv
+ANDEAN ARC part2.csv
+APENNINIC-MAGHREBIDES CHAIN.csv
+BANDA ARC.csv
+BETIC-RIF OROGENIC BELT OR GIBRALTAR ARC.csv
+BISMARCK ARC - NEW BRITAIN ARC.csv
+CASCADES.csv
+CENTRAL AMERICAN VOLCANIC ARC.csv
+CHAGAI-RASKOH ARC.csv
+GREATER ANTILLES.csv
+HALMAHERA ARC.csv
+HONSHU ARC part1.csv
+HONSHU ARC part2.csv
+IZU-BONIN ARC.csv
+KAMCHATKA ARC.csv
+KERMADEC ARC.csv
+KOHISTAN-LADAKH TERRANE OR GANGDISE BELT.csv
+KURILE ARC.csv
+KYUSHU-PALAU RIDGE.csv
+LESSER ANTILLES.csv
+LIGURIA-SARDO-TYRRHENIAN ARC.csv
+LUZON ARC.csv
+MARIANA ARC.csv
+MEXICAN VOLCANIC BELTS.csv
+MIDDLE AMERICA TRENCH - GUATEMALA TRENCH.csv
+NEW HEBRIDES ARC - VANUATU ARCHIPELAGO.csv
+NEW ZEALAND.csv
+OKHOTSK-CHUKOTKA ARC.csv
+RYUKYU ARC.csv
+SCOTIA ARC.csv
+SIKHOTE-ALIN-SAKHALIN ARC.csv
+SOLOMON ISLAND ARC.csv
+SULAWESI ARC.csv
+SUNDA ARC.csv
+TALKEETNA ARC.csv
+TONGA ARC.csv
+WESTERN ALPS.csv
+YAP ARC.csv
+YEMEN PLATEAU.csv

pyrolite/data/georoc/GEOROC_OIB_Dataset_List.csv

@@ -0,0 +1,49 @@
+AHU VOLCANIC FIELD.csv
+AMSTERDAM-ST PAUL.csv
+ASCENSION.csv
+AUSTRAL-COOK ISLANDS.csv
+AZORES.csv
+BALLENY ISLANDS.csv
+BOUVET.csv
+CAMEROON LINE.csv
+CANARY ISLANDS.csv
+CAPE VERDE ISLANDS.csv
+CAROLINE ISLANDS.csv
+CHRISTMAS ISLAND SEAMOUNT PROVINCE.csv
+COCOS ISLAND.csv
+COMOROS.csv
+CROZET ISLANDS.csv
+DESVENTURADOS ISLANDS.csv
+EASTER SEAMOUNT CHAIN - SALAS Y GOMEZ RIDGE.csv
+FERNANDO DE NORONHA ARCHIPELAGO.csv
+GALAPAGOS ISLANDS.csv
+GOUGH CHAIN.csv
+HAWAIIAN-EMPEROR CHAIN.csv
+HAWAIIAN ARCH VOLCANIC FIELDS.csv
+HAWAIIAN ISLANDS part1.csv
+HAWAIIAN ISLANDS part2.csv
+HEARD.csv
+ICELAND.csv
+JAN MAYEN.csv
+JUAN FERNANDEZ ISLANDS.csv
+KERGUELEN.csv
+MADEIRA ARCHIPELAGO.csv
+MARION ISLANDS.csv
+MARQUESAS.csv
+MASCARENE ISLANDS INCL REUNION.csv
+MCDONALD ISLANDS.csv
+PETER I ISLAND.csv
+PITCAIRN-GAMBIER CHAIN.csv
+PRINCE EDWARD ISLANDS.csv
+REVILLAGIGEDO ARCHIPELAGO.csv
+ROSS ISLAND.csv
+SAMOAN ISLANDS.csv
+SCOTT ISLAND.csv
+SELVAGEN ISLANDS.csv
+SOCIETY ISLANDS.csv
+ST HELENA CHAIN.csv
+TRINDADE-VITORIA RISE.csv
+TRISTAN DA CUNHA GROUP.csv
+TUAMOTU ISLANDS.csv
+TUPA VOLCANIC FIELD.csv
+UMU VOLCANIC FIELD.csv

pyrolite/data/georoc/GEOROC_OceanicPlateau_Dataset_List.csv

@@ -0,0 +1,18 @@
+BERMUDA RISE.csv
+BRAZIL BASIN.csv
+CAPE VERDE RISE.csv
+CARIBBEAN-COLOMBIAN PLATEAU.csv
+CUVIER OR WALLABY PLATEAU.csv
+HESS RISE.csv
+HIKURANGI PLATEAU.csv
+KERGUELEN PLATEAU.csv
+MAGELLAN RISE.csv
+MANIHIKI PLATEAU.csv
+MASCARENE PLATEAU.csv
+MATSUMAE PLATEAU.csv
+MAUD RISE.csv
+NATURALISTE PLATEAU.csv
+ONTONG JAVA.csv
+RIO GRANDE RISE.csv
+SAO PAULO PLATEAU.csv
+SHATSKY RISE.csv

pyrolite/geochem.py

@@ -4,8 +4,8 @@
 import periodictable as pt
 import matplotlib.pyplot as plt
 import functools
-from .compositions import renormalise
-from .normalisation import ReferenceCompositions, RefComp
+from .comp import renormalise
+from .norm import ReferenceCompositions, RefComp
 from .util.text import titlecase
 from .util.pd import to_frame
 from .util.math import *

pyrolite/normalisation.py → pyrolite/norm.py

@@ -3,7 +3,7 @@
 import platform
 import pandas as pd
 import numpy as np
-from .compositions import *
+from .comp import *
 from .util.pd import to_frame, to_numeric
 import logging
 

pyrolite/util/general.py

@@ -1,11 +1,9 @@
 import os, sys
-import subprocess
-import shutil
-import zipfile
-import inspect
 import re
-from itertools import chain
+import subprocess, shutil
 import operator
+import inspect
+import zipfile
 from collections import Mapping
 from pathlib import Path
 import numpy as np
@@ -36,7 +34,7 @@ def pathify(path):
     if not isinstance(path, Path):
         path = Path(path)
     return path
-    
+
 
 def urlify(url):
     """Strip a string to return a valid URL."""

pyrolite/util/georoc.py

@@ -4,11 +4,11 @@
 import re
 import logging
 
-from pyrolite.util.pd import *
-from pyrolite.util.text import titlecase, parse_entry, split_records
-from pyrolite.util.general import temp_path, urlify, pyrolite_datafolder, \
+from ..util.pd import *
+from ..util.text import titlecase, parse_entry, split_records
+from ..util.general import temp_path, urlify, pyrolite_datafolder, \
                                   pathify
-from pyrolite.geochem import tochem, check_multiple_cation_inclusion, \
+from ..geochem import tochem, check_multiple_cation_inclusion, \
                              aggregate_cation
 
 logging.getLogger(__name__).addHandler(logging.NullHandler())

setup.cfg

@@ -2,7 +2,7 @@
 test=pytest
 
 [tool:pytest]
-addopts = --cov-report term-missing --cov-report html --cov-config .coveragerc --cov=pyrolite
+addopts = --cov-report term-missing --cov-report html --cov-config .coveragerc --cov=pyrolite --ignore=draft
 
 [versioneer]
 VCS = git

test/compositions/test_compositions_aggregate.py → test/comp/test_comp_aggregate.py

@@ -1,6 +1,6 @@
 import unittest
 import numpy as np
-from pyrolite.compositions.aggregate import *
+from pyrolite.comp.aggregate import *
 from pyrolite.util.pd import test_df
 
 import logging

test/compositions/test_compositions_codata.py → test/comp/test_comp_codata.py

@@ -1,6 +1,6 @@
 import unittest
 import numpy as np
-from pyrolite.compositions.codata import *
+from pyrolite.comp.codata import *
 from pyrolite.util.pd import test_df
 import logging
 log = logging.getLogger(__name__)

test/compositions/test_compositions_impute.py → test/comp/test_comp_impute.py

@@ -2,8 +2,8 @@
 import numpy as np
 import pandas as pd
 from pyrolite.util.pd import test_df, test_ser
-from pyrolite.compositions.aggregate import np_cross_ratios
-from pyrolite.compositions.impute import *
+from pyrolite.comp.aggregate import np_cross_ratios
+from pyrolite.comp.impute import *
 
 
 class TestPDImputeRatios(unittest.TestCase):

test/test_classification.py

@@ -1,6 +1,6 @@
 import unittest
 from pyrolite.classification import *
-from pyrolite.compositions import renormalise
+from pyrolite.comp import renormalise
 
 
 class TestTAS(unittest.TestCase):

test/test_geochem.py

@@ -3,7 +3,7 @@
 import numpy as np
 from pyrolite.geochem import *
 from pyrolite.util.pd import test_df, test_ser
-from pyrolite.normalisation import ReferenceCompositions
+from pyrolite.norm import ReferenceCompositions
 
 
 class TestGetRadii(unittest.TestCase):

test/test_normalisation.py → test/test_norm.py

@@ -1,6 +1,6 @@
 import unittest
 import pyrolite
-from pyrolite.normalisation import *
+from pyrolite.norm import *
 
 
 class TestScaleFunction(unittest.TestCase):
@@ -75,12 +75,10 @@ class TestRefcomp(unittest.TestCase):
 
     def setUp(self):
         self.build_kwargs = dict(encoding='cp1252')
-        pyrodir = os.path.realpath(pyrolite.normalisation.__file__)
+        pyrodir = os.path.realpath(pyrolite.__file__)
         self.dir = (Path(pyrodir).parent /  "data" / "refcomp").resolve()
         assert self.dir.is_dir()
         self.files = [x for x in self.dir.iterdir() if x.is_file()]
-
-        print(self.dir, self.files)
         self.CHfile = [f for f in self.files
                        if 'CH_PalmeONeill2014' in str(f)][0]
 

test/util/test_util_math.py

@@ -72,13 +72,13 @@ def test_orthagonal_basis(self):
         """Checks orthagonality of the transformation basis."""
         pass
 
-        
+
 class TestOPConstants(unittest.TestCase):
     """Checks the generation of orthagonal polynomial parameters."""
 
     def setUp(self):
         self.xs = np.array(get_radii(REE()))
-        self.default_degree = 5
+        self.default_degree = 4
 
     def test_xs(self):
         """Tests operation on different x arrays."""
@@ -91,7 +91,7 @@ def test_xs(self):
     def test_degree(self):
         """Tests generation of different degree polynomial parameters."""
 
-        max_degree = 5
+        max_degree = 4
         expected = OP_constants(self.xs, degree=max_degree)
         for degree in range(1, max_degree):
             with self.subTest(degree=degree):

test/util/test_util_plot.py

@@ -1,14 +1,15 @@
 import unittest
+from pathlib import Path
 import pandas as pd
 import numpy as np
+import matplotlib
 import matplotlib.axes as matax
 import matplotlib.pyplot as plt
+from sklearn.decomposition import PCA
+
+from pyrolite.comp import close
 from pyrolite.util.plot import *
 from pyrolite.util.general import remove_tempdir
-from sklearn.decomposition import PCA
-from pyrolite.compositions import close
-import matplotlib
-from pathlib import Path
 
 
 class TestAddColorbar(unittest.TestCase):
@@ -162,7 +163,7 @@ def test_get_full_extent(self):
 
     def tearDown(self):
         plt.close('all')
-        
+
 
 class TestSaveFunctions(unittest.TestCase):
     """