cmflow 0.1.1.dev55__tar.gz → 0.3.1__tar.gz

cmflow-0.3.1/.github/workflows/pypi.yml

@@ -0,0 +1,32 @@
+name: Publish on PyPI
+
+on:
+  push:
+    branches:
+      - 'develop'
+      - 'master'
+
+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.dev55 → cmflow-0.3.1}/.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-0.3.1/.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-0.3.1/PKG-INFO

@@ -0,0 +1,152 @@
+Metadata-Version: 2.4
+Name: cmflow
+Version: 0.3.1
+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.dev55 → cmflow-0.3.1}/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
 
@@ -53,9 +49,11 @@ A BMStats object can be reused (very fast) to eg.
     
     # 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
 
@@ -117,3 +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/*
+```