cmflow 0.1.1.dev57__tar.gz → 0.3.2__tar.gz

cmflow-0.3.2/.github/workflows/pypi.yml

@@ -0,0 +1,31 @@
+name: Publish on PyPI
+
+on:
+  push:
+    tags:
+      - 'v*'
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.13]
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.13'
+      - name: Install Hatch
+        run: |
+          python -m pip install --upgrade pip hatch
+      - name: Build and publish on PyPI
+        env:
+          HATCH_INDEX_USER: __token__
+          HATCH_INDEX_AUTH: ${{ secrets.PYPI_PASSWORD }}
+        run: |
+          hatch build
+          hatch publish --no-prompt dist/*

{cmflow-0.1.1.dev57 → cmflow-0.3.2}/.github/workflows/unittest.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [2.7]
+        python-version: [3.13]
     steps:
     - uses: actions/checkout@v1
     - name: Set up Python ${{ matrix.python-version }}
@@ -31,12 +31,7 @@ jobs:
         pip install matplotlib
         pip install shapely
         pip install rtree
-        pip install descartes
-        mkdir pytough
-        cd pytough
-        git clone https://github.com/acroucher/PyTOUGH.git .
-        pip install .
-        cd ..
+        pip install pytough
     - name: Unit tests
       env:
         TWINE_USERNAME: __token__

cmflow-0.3.2/.gitignore

@@ -0,0 +1,33 @@
+*.pyc
+*.pyo
+*.npy
+*.dat
+*.json
+*.incon
+*.png
+*.csv
+*.xyz
+
+# Sphinx
+doc/source/reference/api/
+
+# Files created by releasenotes build
+releasenotes/build
+
+# Packages/installer info
+*.eggs
+*.egg
+*.egg-info
+dist
+build
+
+# Other
+AUTHORS
+ChangeLog
+
+# Editor files
+*~
+*.swp
+
+# virtualenv
+env_*/

cmflow-0.3.2/PKG-INFO

@@ -0,0 +1,152 @@
+Metadata-Version: 2.4
+Name: cmflow
+Version: 0.3.2
+Summary: Building TOUGH2/Waiwera models from layers of conceptual models
+Project-URL: Homepage, https://github.com/cyeh015/cmflow
+Project-URL: Source Code, https://github.com/cyeh015/cmflow
+Author-email: Angus Yeh <a.yeh@auckland.ac.nz>
+Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.8
+Requires-Dist: pytough
+Requires-Dist: rtree
+Requires-Dist: shapely
+Description-Content-Type: text/markdown
+
+# Install
+
+    pip install -U cmflow
+
+# Install Dependency
+
+On most platforms, you should be able to install these packages by:
+
+    pip install shapely
+    pip install rtree
+    pip install pytough
+
+On Linux (Ubuntu shown here) these can be installed via apt-get:
+
+    sudo apt-get install -y python-shapely
+    sudo apt-get install -y python-rtree
+
+# Example
+
+Creates BMStats that can be used later, from Leapfrog Geology:
+
+    # (ONLY ONCE) geo used to get geology from Leapfrog geological model
+    cmgeo = mulgrid('g_very_fine.dat')
+    
+    # CSV file created by Leapfrog using cmgeo above
+    leapfrog = LeapfrogGM()
+    leapfrog.import_leapfrog_csv('grid_gtmp_ay2017_03_6_fit.csv')
+    
+    cm_geology = CM_Blocky(cmgeo, leapfrog)
+    
+    # whatever active model we are working on
+    bmgeo = mulgrid('gwaixx_yy.dat')
+    
+    bms_geology = cm_geology.calc_bmstats(bm_geo)
+    bms_geology.save('a.json')
+
+A BMStats object can be reused (very fast) to eg.
+
+    bms_geology = BMStats('a.json')
+    
+    # get a cell's stats
+    cs = bms_geology.cellstats['abc12']
+    
+    # rock that occupies most in cell 'abc12'
+    rock_name = bms_geology.zones[np.argmax(cs)]
+    
+    # how many rock in cell 'abc12'
+    n_rock = len(np.nonzero(cs))
+    
+    # list all rocks in cell 'abc12'
+    rocks = [bm_geology.zones[i] for i in np.nonzero(cs)]
+    
+    # find all blocks intersect with the zone
+    blocks, ratios = bm_geology.blocks_in_zone('BASE1')
+    block_idx, ratios = bm_geology.blocks_in_zone('BASE1', indices=True)
+    
+
+# BMStats
+
+This is the object that we keep for later use.  It is associated to a certain
+"geometry" file.  So each cell has information on zones. Usually this is
+generated by cm.populate_model(), which can be expensive.
+
+- ? should I call it CMStats?
+- ? TODO, .cellstats access by cell index
+- ? TODO, .
+
+Base Model Stats, mainly numpy arrays with rows corresponding to mulgrid
+blocks, and columns corresponding to zones.  Each is a value, usually
+between 0.0 and 1.0.  Often 1.0 is indicating that particular block is fully
+within the zone.
+
+.stats numpy array (n,m), n = num of model blocks, m = num of zones
+.zones list of zone names (str)
+.zonestats dict of stats column by zone names
+.cellstats dict of stats row by block name
+
+    6 elements, 3 zones
+     A    B    C
+    0.0, 0.7, 0.3,  -> row sum to 1.0, element 0, 0.7 rock B, 0.3 rock C 
+    1.0, 0.0, 0.0, 
+    1.0, 0.0, 0.0, 
+    0.0, 0.5, 0.5, 
+    0.1, 0.2, 0.7, 
+    0.0, 1.0, 0.0, 
+    (this is only one way of using it, such as a rocktype)
+
+.stats, numpy array (n * m), n number of geometry cells, m number of zones
+.zones, a list of zone name, eg. geology rock names, fault names etc
+.zonestats, a dict keyed by zone name, an array of size number of cells, each cell is between 
+.cellstats, a dict of stats by cell name
+
+.save()
+.load()
+.add_stats() add another bmstat, merge stats
+.add_cm() calls cm.populate_model, and merge stats
+
+# CM
+# CM_Blocky
+# CM_Prism
+# CM_Faults
+
+These are the objects that can be created in order to create the final BMStats
+objects.  The common method .populate_model(bm_geo) is called to create BMStats
+objects.  It means the conceptual model is "applied" onto the bm_geo.
+
+- TODO, .populate_model() should return BMStats instead
+- ? TODO, .populate_model() should be called something else?
+
+.populate_model(bm_geo) takes a target geometry, and return/creates BMStats
+
+
+# LeapfrogGM
+
+
+
+
+# Build and Publish
+
+To bump version, create a tag, eg. `v0.1.0`.
+
+If upload for the first time, create a PyPI account token, then use it for the publish step. The PyPI project will be created on first upload. Then revoke the account token and create a project token for later publishes.
+
+Publish to PyPI:
+
+```console
+hatch build
+hatch publish dist/*
+```

{cmflow-0.1.1.dev57 → cmflow-0.3.2}/README.md

@@ -4,20 +4,16 @@
 
 # Install Dependency
 
-On Windows, `Shapely` and `Rtree` are easier to be installed by using Christoph Gohlke's non-official build: 
+On most platforms, you should be able to install these packages by:
 
-- [https://www.lfd.uci.edu/~gohlke/pythonlibs/#shapely](https://www.lfd.uci.edu/~gohlke/pythonlibs/#shapely)
-- [https://www.lfd.uci.edu/~gohlke/pythonlibs/#rtree](https://www.lfd.uci.edu/~gohlke/pythonlibs/#rtree)
-
-`descartes` can be installed on all platform by:
-
-    pip install descartes
+    pip install shapely
+    pip install rtree
+    pip install pytough
 
 On Linux (Ubuntu shown here) these can be installed via apt-get:
 
     sudo apt-get install -y python-shapely
     sudo apt-get install -y python-rtree
-    sudo apt-get install -y python-descartes
 
 # Example
 
@@ -119,3 +115,15 @@ objects.  It means the conceptual model is "applied" onto the bm_geo.
 
 
 
+# Build and Publish
+
+To bump version, create a tag, eg. `v0.1.0`.
+
+If upload for the first time, create a PyPI account token, then use it for the publish step. The PyPI project will be created on first upload. Then revoke the account token and create a project token for later publishes.
+
+Publish to PyPI:
+
+```console
+hatch build
+hatch publish dist/*
+```

{cmflow-0.1.1.dev57 → cmflow-0.3.2}/cmflow/conceptual_models.py

@@ -8,10 +8,9 @@ from shapely.geometry import Polygon
 from shapely.geometry import LineString
 
 # for faults CM
-from geom_3dface_utils import Face3D
-#
-from geom_surface_utils import get_columns_intersect_polygon
-from geom_surface_utils import geo_column_polygon
+from cmflow.geom_3dface_utils import Face3D
+from cmflow.geom_surface_utils import get_columns_intersect_polygon
+from cmflow.geom_surface_utils import geo_column_polygon
 
 import json
 import time
@@ -20,9 +19,9 @@ START = [time.time()]
 def print_wall_time(msg, loop_stop=False, total=False):
     t = time.time()
     if total:
-        print msg, ': %f seconds' % (t - START[0])
+        print(msg, ': %f seconds' % (t - START[0]))
     else:
-        print msg, ': %f seconds' % (t - START[-1])
+        print(msg, ': %f seconds' % (t - START[-1]))
     if loop_stop:
         START.append(t)
 
@@ -32,7 +31,7 @@ class LeapfrogGM(object):
         self.litholist = []
         self.blocklitho = {}
         self.import_from = '' # optional, if imported from leapfrog
-        self.geometry = '' # optional, matching mulgrid geometry file
+        self.geometry = geometry # optional, matching mulgrid geometry file
 
     def import_leapfrog_csv(self, filename, report=False):
         """ load geology info from Leapfrog's 'Generate rock types' feature.  The
@@ -62,13 +61,13 @@ class LeapfrogGM(object):
                 self.litholist.append(row[2])
                 lithocodes[int(row[1])] = len(self.litholist)-1
             if read_block_litho:
-                if len(row) <> 2: break
+                if len(row) != 2: break
                 self.blocklitho[row[0]] = lithocodes[int(row[1])]
         f.close()
         self.import_from = filename
         if report:
-            print '%8s Lithology found.' % len(self.litholist)
-            print '%8s Blocks allocated.' % len(self.blocklitho)
+            print('%8s Lithology found.' % len(self.litholist))
+            print('%8s Blocks allocated.' % len(self.blocklitho))
 
     def write(self, filename):
         with open(filename, 'w') as f:
@@ -365,7 +364,7 @@ class CM_Faults(CM):
         if isinstance(dilation, float):
             if dilation > 0.0:
                 self.dilation = dilation
-                print 'Fault uses dilation'
+                print('Fault uses dilation')
         if faults is None:
             pass
         elif isinstance(faults, list):
@@ -446,7 +445,7 @@ class CM_Faults(CM):
                 if len(pts) < 2:
                     # not enough points to construct LineString, layer not
                     # cutting through the fault Face
-                    print "    skipping layer %i '%s' with fault '%s'" % (jj, lay.name, fname)
+                    print("    skipping layer %i '%s' with fault '%s'" % (jj, lay.name, fname))
                     continue
                 line = LineString([tuple(pt[:2]) for pt in pts])
                 if self.dilation is not None:
@@ -623,139 +622,6 @@ class BMStats(object):
         else:
             return nbs, nrs
 
-def test_zonestats_small():
-    from t2data_utils import create_basic_t2data, update_block_geology
-    START = [time.time()]
-    geo = mulgrid().rectangular([1000]*20, [1000]*20, [100]*5, origin=[0,0,0],
-                                 atmos_type=0)
-    stats = BMStats(geo)
-    poly = Polygon([
-        np.array([1147.7 , 14125.4]),
-        np.array([487.0  , 13041.7]),
-        np.array([302.0  , 11799.4]),
-        np.array([592.7  , 10372.2]),
-        np.array([1412.1 , 8389.8]),
-        np.array([1993.5 , 7808.4]),
-        np.array([2865.8 , 7729.1]),
-        np.array([3685.1 , 7544.1]),
-        np.array([3975.9 , 6460.4]),
-        np.array([4002.3 , 3262.2]),
-        np.array([3923.0 , 2020.0]),
-        np.array([3685.1 , 1094.9]),
-        np.array([5720.3 , 275.5]),
-        np.array([6645.4 , 381.3]),
-        np.array([7914.1 , 698.4]),
-        np.array([9156.3 , 857.0]),
-        np.array([9922.8 , 804.2]),
-        np.array([11693.7, 1676.4]),
-        np.array([12486.6, 2786.5]),
-        np.array([12539.5, 4927.4]),
-        np.array([13913.9, 7121.2]),
-        np.array([13543.9, 8680.6]),
-        np.array([11376.5, 8574.9]),
-        np.array([9473.5 , 8522.0]),
-        np.array([8072.7 , 8944.9]),
-        np.array([7121.1 , 10160.7]),
-        np.array([6989.0 , 11244.4]),
-        np.array([6856.8 , 11905.2]),
-        np.array([5641.0 , 13041.7]),
-        np.array([4980.2 , 13358.9]),
-        np.array([3711.6 , 14204.7]),
-        np.array([3262.2 , 14733.3]),
-        np.array([1967.1 , 14812.6]),
-        np.array([1359.2 , 14389.7]),
-        ])
-    ztop, zbot = 0.0, -100.0
-    cm = CM_Prism('resis', poly, ztop, zbot)
-    stats.add_cm(cm)
-    ztop, zbot = -200.0, -300.0
-    cm = CM_Prism('resis', poly, ztop, zbot)
-    stats.add_cm(cm)
-    stats.save('tmp_cm.json')
-    stats_2 = BMStats(geo)
-    stats_2.load('tmp_cm.json')
-    # check if the same
-    assert stats.zones == stats_2.zones
-    assert np.array_equal(stats.stats, stats_2.stats)
-    dat = create_basic_t2data(geo)
-
-    # starting with single rock deflt
-    orig_name = dat.grid.rocktypelist[0].name
-    dat.grid.rename_rocktype(orig_name, 'NA   ') # not in geological model
-    # ATMOS
-    for i in range(dat.grid.num_atmosphere_blocks):
-        update_block_geology(dat, dat.grid.blocklist[i].name, 'ATMOS')
-    # others
-    for i in range(dat.grid.num_atmosphere_blocks, dat.grid.num_blocks):
-        zi = np.argmax(stats.stats[i,:])
-        if stats.stats[i,zi] > 0.0:
-            # print CM_0_stats[i,zi], CM_0_stats[i,:]
-            new_rname = update_block_geology(dat, dat.grid.blocklist[i].name, stats.zones[0])
-    geo.write('gtmp.dat')
-    dat.write('tmp.dat')
-
-def test_cm_blocky_full():
-    START = [time.time()]
-
-    leapfrog = LeapfrogGM(geometry='gtmp_ay2017_03_6')
-    leapfrog.import_leapfrog_csv('grid_gtmp_ay2017_03_6_fit.csv')
-    leapfrog.write('_leapfrog.json')
-    print_wall_time('loaded leapfrog GM', loop_stop=True)
-
-    geo = mulgrid('gtmp_ay2017_03_6_fit.dat')
-    print_wall_time('loaded CM geo', loop_stop=True)
-
-    bm_geo = mulgrid('gtmp_ay2017_05_5a.dat')
-    print_wall_time('loaded CM geo and BM geo', loop_stop=True)
-
-    print '  CM has %i blocks: %s' % (geo.num_blocks, geo.filename)
-    print '  BM has %i blocks: %s' % (bm_geo.num_blocks, bm_geo.filename)
-
-    cm = CM_Blocky(geo, leapfrog)
-    stats, zones = cm.populate_model(bm_geo)
-
-    print_wall_time('Finished all, total wall time:', total=True)
-
-    print np.nonzero(stats)
-    np.save('_CM_results.npy', stats)
-
-    with open('_CM_results.json', 'w') as f:
-        json.dump({
-                    "comments": [
-                        "CM (leapfrog): " + leapfrog.import_from,
-                        "CM geometry: " + geo.filename,
-                        "BM geometry: " + bm_geo.filename,
-                    ],
-                    "zones": zones,
-                    "stats": stats.tolist(),
-                  }, f, indent=4, sort_keys=True)
-
-
-def test_cm_fault_full():
-    import glob
-    START = [time.time()]
-
-    bm_geo = mulgrid('gtmp_ay2017_05_5a.dat')
-    print_wall_time('loaded BM geo', loop_stop=True)
-    print '  BM has %i blocks: %s' % (bm_geo.num_blocks, bm_geo.filename)
-
-    cm_f = CM_Faults(sorted(glob.glob('*.ts')))
-    print_wall_time('loaded faults CM w/ %i faults' % cm_f.num_zones, loop_stop=True)
-
-    stats, zones = cm_f.populate_model(bm_geo)
-    print_wall_time('Finished all, total wall time:', total=True)
-
-    save_as = '_CM_faults_results'
-    print np.nonzero(stats)
-    np.save(save_as + '.npy', stats)
-    with open(save_as + '.json', 'w') as f:
-        json.dump({
-                    "comments": [
-                        "BM geometry: " + bm_geo.filename,
-                    ],
-                    "zones": zones,
-                    "stats": stats.tolist(),
-                  }, f, indent=4, sort_keys=True)
 
 
 if __name__ == '__main__':

{cmflow-0.1.1.dev57 → cmflow-0.3.2}/cmflow/geom_3dface_utils.py

@@ -163,38 +163,38 @@ class Face3D(object):
 
     def read(self, filename):
         # TODO: implement full support, see http://paulbourke.net/dataformats/gocad/gocad.pdf
-        f = open(filename, 'r')
-        if not f.next().startswith('GOCAD TSurf 1'):
-            raise Exception("File type not supported, need .ts file starts with 'GOCAD TSurf 1'.")
-        done = False
-        for line in f:
-            if line.startswith('HEADER'):
-                line = f.next()
-                while '}' not in line:
-                    c = line.strip().split(':')
-                    self.header[c[0]] = c[1]
-                    line = f.next()
-            elif line.startswith('TFACE'):
-                print 'Reading TFACE...',
-                for line in f:
-                    if line.startswith('PVRTX'):
-                        c = line.strip().split()
-                        self.points[c[1]] = Point(c[1], [float(x) for x in c[2:]])
-                    if line.startswith('TRGL'):
-                        c = line.strip().split()
-                        self.triangles.append(Triangle([self.points[p] for p in c[1:]]))
-                        # add back references
-                        self.triangles[-1].index = len(self.triangles) - 1
-                        for p in c[1:]:
-                            self.points[p].in_triangles.append(self.triangles[-1])
-                    if line.startswith('END'):
-                        done = True
-                        break
-            else:
-                pass
-        f.close()
+        with open(filename, 'r') as f:
+            first_line = f.readline()
+            if not first_line.startswith("GOCAD TSurf 1"):
+                raise ValueError("File type not supported, need .ts file starts with 'GOCAD TSurf 1'.")
+            done = False
+            for line in f:
+                if line.startswith('HEADER'):
+                    line = next(f)
+                    while '}' not in line:
+                        c = line.strip().split(':')
+                        self.header[c[0]] = c[1]
+                        line = next(f)
+                elif line.startswith('TFACE'):
+                    print('Reading TFACE...', end=' ')
+                    for line in f:
+                        if line.startswith('PVRTX'):
+                            c = line.strip().split()
+                            self.points[c[1]] = Point(c[1], [float(x) for x in c[2:]])
+                        if line.startswith('TRGL'):
+                            c = line.strip().split()
+                            self.triangles.append(Triangle([self.points[p] for p in c[1:]]))
+                            # add back references
+                            self.triangles[-1].index = len(self.triangles) - 1
+                            for p in c[1:]:
+                                self.points[p].in_triangles.append(self.triangles[-1])
+                        if line.startswith('END'):
+                            done = True
+                            break
+                else:
+                    pass
         if done:
-            print 'Done.'
+            print('Done.')
 
     def __repr__(self):
         if 'name' in self.header:
@@ -244,14 +244,14 @@ class Face3D(object):
         # cur_ep can be either a segment or a point
         if isect['itype'] == (0,2):
             # two edges crosses plane
-            ks = isect['crosses'].keys()
+            ks = list(isect['crosses'].keys())
             cur_ep, other_end_ep = ks[0], ks[1]
         elif isect['itype'] == (2,0):
             # two corners on plane
             cur_ep, other_end_ep = isect['corners'][0], isect['corners'][1]
         else:
             # one corner on plane, one edge crosses plane
-            ks = isect['crosses'].keys()
+            ks = list(isect['crosses'].keys())
             cur_ep, other_end_ep = isect['corners'][0], ks[0]
 
         line = [self.get_intersection_co(other_end_ep, isect), self.get_intersection_co(cur_ep, isect)]
@@ -297,7 +297,7 @@ class Face3D(object):
 
             isect = self.cached_tri_intersections[nbs[0].index]
             exits = []
-            for ex in isect['crosses'].keys() + isect['corners']:
+            for ex in list(isect['crosses'].keys()) + isect['corners']:
                 if isinstance(cur_ep, tuple):
                     if ex in [cur_ep, cur_ep[::-1]]:
                         continue