Merge branch 'release/0.1.19'

CHANGELOG

@@ -0,0 +1,60 @@
+# Changelog
+All notable changes to this project will be documented in this file.
+
+## [Unreleased]
+
+## [0.1.18]
+
+## [0.1.17]
+
+## [0.1.16]
+
+## [0.1.15]
+
+## [0.1.14]
+
+## [0.1.13]
+
+## [0.1.12]
+
+## [0.1.11]
+
+## [0.1.10]
+
+## [0.1.9]
+
+## [0.1.8]
+
+## [0.1.7]
+
+## [0.1.6]
+
+## [0.1.5]
+
+## [0.1.4]
+
+## [0.1.2]
+
+## [0.1.1]
+
+## [0.1.0]
+
+[Unreleased]: https://github.com/morganjwilliams/pyrolite/compare/0.1.18...develop
+[0.1.18]: https://github.com/morganjwilliams/pyrolite/compare/0.1.17...0.1.18
+[0.1.17]: https://github.com/morganjwilliams/pyrolite/compare/0.1.16...0.1.17
+[0.1.16]: https://github.com/morganjwilliams/pyrolite/compare/0.1.15...0.1.16
+[0.1.15]: https://github.com/morganjwilliams/pyrolite/compare/0.1.14...0.1.15
+[0.1.14]: https://github.com/morganjwilliams/pyrolite/compare/0.1.13...0.1.14
+[0.1.13]: https://github.com/morganjwilliams/pyrolite/compare/0.1.12...0.1.13
+[0.1.12]: https://github.com/morganjwilliams/pyrolite/compare/0.1.11...0.1.12
+[0.1.11]: https://github.com/morganjwilliams/pyrolite/compare/0.1.10...0.1.11
+[0.1.10]: https://github.com/morganjwilliams/pyrolite/compare/0.1.9...0.1.10
+[0.1.9]: https://github.com/morganjwilliams/pyrolite/compare/0.1.8...0.1.9
+[0.1.8]: https://github.com/morganjwilliams/pyrolite/compare/0.1.7...0.1.8
+[0.1.7]: https://github.com/morganjwilliams/pyrolite/compare/0.1.6...0.1.7
+[0.1.6]: https://github.com/morganjwilliams/pyrolite/compare/0.1.5...0.1.6
+[0.1.5]: https://github.com/morganjwilliams/pyrolite/compare/0.1.4...0.1.5
+[0.1.4]: https://github.com/morganjwilliams/pyrolite/compare/0.1.2...0.1.4
+[0.1.2]: https://github.com/morganjwilliams/pyrolite/compare/0.1.1...0.1.2
+[0.1.1]: https://github.com/morganjwilliams/pyrolite/compare/0.1.0...0.1.1
+[0.1.0]: https://github.com/morganjwilliams/pyrolite/compare/0.0.17...0.1.0

MANIFEST.in

@@ -1,4 +1,12 @@
 include versioneer.py
 include pyrolite/_version.py
 include LICENSE
-recursive-include pyrolite/data *
+recursive-include pyrolite/data/Aitchison *
+include pyrolite/data/alphamelts/env.py
+recursive-include pyrolite/data/geochem *
+recursive-include pyrolite/data/models *
+recursive-include pyrolite/data/refcomp *
+recursive-include pyrolite/data/shannon *
+recursive-include pyrolite/data/timescale *
+exclude pyrolite/data/alphamelts/localinstall
+global-exclude __pycache__

docs/examples/alphamelts/automation.py

@@ -5,7 +5,13 @@
 import numpy as np
 from pyrolite.util.synthetic import test_df
 
-df = test_df(cols=["SiO2", "CaO", "MgO", "FeO", "TiO2", "Na2O", "K2O", "P2O5"]) * 100
+df = (
+    test_df(
+        cols=["SiO2", "CaO", "MgO", "FeO", "TiO2", "Na2O", "K2O", "P2O5"],
+        index_length=5,
+    )
+    * 100
+)
 df["Sample"] = np.arange(df.index.size)
 # %% setup environment
 from pyrolite.ext.alphamelts.env import MELTS_Env
@@ -17,9 +23,6 @@
 env.MINP = 2000
 env.DELTAT = -3
 
-with open("pyrolite_envfile.txt", "w") as f:  # write the environment to a file
-    f.write(env.to_envfile(unset_variables=False))
-# %% setup dataframe
 # taking a dataframe with oxide/element headers, set up experiment info
 df["Title"] = df.Sample
 df["Initial Pressure"] = 7000
@@ -34,11 +37,13 @@
         df.loc[ix, :],  # take the specific row
         writetraces=False,  # ignore trace element data
         modes=[
-            "isobaric",
+            "isenthalpic",
             "fractionate solids",
         ],  # conduct an isobaric experiment where solids are fractionated
         exclude=["P2O5", "K2O"],  # exclude potassium and phosphorous
     )
     # create an experiment folder to work in, add the meltsfile and environment file
-    exp = MeltsExperiment(meltsfile=meltsfile, title=str(df.loc[ix, "Title"]), env=env)
+    exp = MeltsExperiment(
+        meltsfile=meltsfile, title="test" + str(df.loc[ix, "Title"]), env=env
+    )
     exp.run(superliquidus_start=True)

docs/examples/alphamelts/meltsweb.py

@@ -0,0 +1,35 @@
+from pyrolite.ext.alphamelts.web import *
+
+
+def default_datadict():
+    d = {}
+    d["title"] = ("TestREST",)
+    d["initialize"] = {
+        "SiO2": 48.68,
+        "TiO2": 1.01,
+        "Al2O3": 17.64,
+        "Fe2O3": 0.89,
+        "Cr2O3": 0.0425,
+        "FeO": 7.59,
+        "MnO": 0.0,
+        "MgO": 9.10,
+        "NiO": 0.0,
+        "CoO": 0.0,
+        "CaO": 12.45,
+        "Na2O": 2.65,
+        "K2O": 0.03,
+        "P2O5": 0.08,
+        "H2O": 0.20,
+    }
+    d["calculationMode"] = "findLiquidus"
+    d["constraints"] = {"setTP": {"initialT": 1200, "initialP": 1000}}
+    return d
+
+
+D = default_datadict()
+# %% Oxides
+melts_oxides(D)
+# %% Phases
+melts_phases(D)
+# %% Compute
+melts_compute(D)

docs/examples/alphamelts/montecarlo.py

@@ -26,7 +26,7 @@
     ["SiO2", "Al2O3", "FeO", "MnO", "MgO", "CaO", "Na2O", "TiO2", "K2O", "P2O5"],
     "value",
 ]
-MORB
+
 MORB["Title"] = Gale_MORB.ModelName
 MORB["Initial Temperature"] = 1300
 MORB["Final Temperature"] = 800

docs/examples/geochem/convert_chemistry.py

@@ -0,0 +1,20 @@
+from pyrolite.geochem.transform import convert_chemistry
+# %% Random data
+import numpy as np
+import pandas as pd
+from pyrolite.util.synthetic import test_df
+
+np.random.seed(82)
+df = (test_df(cols=["MgO", "SiO2", "FeO", "CaO", "Na2O"]) * 100).join(
+    test_df(cols=["Ca", "Te", "K", "Na"]) * 1000
+)
+# %% Unit Conversion
+from pyrolite.geochem.ind import common_elements
+from pyrolite.geochem.norm import scale
+
+ppm_cols = [i for i in df.columns if i in common_elements()]  # elemental headers
+df.loc[:, ppm_cols] *= scale("ppm", "wt%")
+# Conversion
+new_df = convert_chemistry(
+    df, to=["MgO", "SiO2", "FeO", "CaO", "Te", "Na", "Na/Te", "MgO/SiO2"]
+)

docs/source/submoddoc/ext/alphamelts.rst

@@ -34,6 +34,12 @@ pyrolite\.ext\.alphamelts\.tables
       :members:
       :undoc-members:
 
+pyrolite\.ext\.alphamelts\.plottemplates
+---------------------------------------
+  .. automodule:: pyrolite.ext.alphamelts.plottemplates
+      :members:
+      :undoc-members:
+
 pyrolite\.ext\.alphamelts\.util
 ---------------------------------------
   .. automodule:: pyrolite.ext.alphamelts.util

docs/source/submoddoc/external.rst

@@ -20,10 +20,3 @@ pyrolite\.ext\.datarepo
      :maxdepth: 2
 
      ext/datarepo
-
-
-pyrolite\.ext\.iogas
--------------------------------
-  .. automodule:: pyrolite.ext.iogas
-      :members:
-      :undoc-members:

docs/source/tests.rst

@@ -4,7 +4,8 @@ Tests
 .. seealso:: `Contributing <contributing.html>`__
 
 If you clone the source repository, unit tests can be run using pytest from the root
-directory after installation:
+directory after installation with development dependencies
+(:code:`pip install -e .[dev]`):
 
 .. code-block:: bash
 

docs/source/usage/eg/alphamelts/automation.rst

@@ -8,27 +8,21 @@ especially for established workflows or repetitive calculations.
   :language: python
   :end-before: # %% testdf
 
-First we can configure an environment, which in this case is written to file:
+First we can configure an environment, which in this case is written to file.
+We can then add individual experiment parameters to the :code:`~pandas.DataFrame`:
 
 .. literalinclude:: ../../../../examples/alphamelts/automation.py
   :language: python
   :start-after: # %% setup environment
-  :end-before: # %% setup dataframe
-
-We can then add individual experiment parameters to the dataframe:
-
-.. literalinclude:: ../../../../examples/alphamelts/automation.py
-  :language: python
-  :start-after: # %% setup dataframe
   :end-before: # %% autorun
 
-And finally, we can run an experiment for each composition in the dataframe:
+And finally, we can run an experiment for each composition in the
+:code:`~pandas.DataFrame`:
 
 .. literalinclude:: ../../../../examples/alphamelts/automation.py
   :language: python
   :start-after: # %% autorun
 
-
 .. seealso::
 
   Examples: