pyIntersecT 0.1.3__tar.gz → 0.1.4__tar.gz

{pyintersect-0.1.3 → pyintersect-0.1.4}/IntersecT.ipynb

@@ -21,7 +21,7 @@
     "\n",
     "##### **Requirements**\n",
     "The following Python packages are required. Installation of pyIntersecT through pip will automatically install all necessary dependencies.\n",
-    "- Python 3.9 or higher\n",
+    "- Python 3.10 or higher\n",
     "- matplotlib\n",
     "- pandas\n",
     "- **pyIntersecT**\n",
@@ -151,6 +151,10 @@
     "\n",
     "**Row 1 - Element identifiers:** Specify each element using the format Phase_Element. For example, garnet compositions would be listed as Grt_Mg, Grt_Ca, Grt_Fe, Grt_Mn. If uncertain on the naming, search for the output model naming in the mineral_symbols.toml and use the corresponding abbreviation.\n",
     "\n",
+    "*Iron (Perple_X only):* ferrous and ferric iron can be distinguished only for Perple_X models calculated with Fe2O3 as a system component. Use Grt_Fe for Fe2+ (FeO), Grt_Fe3 for Fe3+ (Fe2O3) and Grt_Fetot for total iron (Fe2+ + Fe3+). Grt_Fetot should be used when the measured iron is not recalculated into Fe2+ and Fe3+.\n",
+    "\n",
+    "*Iron (MAGEMin, or Perple_X with O2):* Grt_Fe refers to total iron, and the measured value must be total iron. Do not use Grt_Fe3 or Grt_Fetot, as the missing model values would exclude the whole phase from the calculation.\n",
+    "\n",
     "**Row 2 - Observed values:** Measured compositional values expressed in atoms per formula unit (a.p.f.u.) corresponding to each element specified in row 1.\n",
     "\n",
     "**Row 3 - Analytical uncertainties:** Either numerical uncertainty values for each measurement or a dash (-) to trigger automatic uncertainty calculation based on the analytical technique specified in row 4.\n",

{pyintersect-0.1.3 → pyintersect-0.1.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyIntersecT
-Version: 0.1.3
+Version: 0.1.4
 Summary: Quantitative isopleth thermobarometry from PerpleX
 Project-URL: Homepage, https://github.com/neoscalc/IntersecT
 Project-URL: Bug Tracker, https://github.com/neoscalc/IntersecT/issues
@@ -682,9 +682,11 @@ License:                     GNU GENERAL PUBLIC LICENSE
 License-File: LICENSE
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3.10
+Requires-Python: >=3.10
 Requires-Dist: matplotlib
 Requires-Dist: numpy
 Requires-Dist: pandas
+Requires-Dist: tomli; python_version < '3.11'
 Description-Content-Type: text/markdown
 
 # IntersecT
@@ -849,7 +851,7 @@ Measured mineral compositions must be provided in a tab-delimited text file. Com
 
 The file follows a specific six-row structure.
 
-**Row 1** specifies element identifiers using Phase_Element format where phase names follow Warr (2021) abbreviations. Consult mineral_symbols.toml to recognise abbreviations and their mappings.
+**Row 1** specifies element identifiers using Phase_Element format where phase names follow Warr (2021) abbreviations. Consult mineral_symbols.toml to recognise abbreviations and their mappings. Ferrous and ferric iron can be distinguished only for Perple_X models calculated with Fe2O3 as a system component. In this case, Phase_Fe refers to Fe2+ (FeO), Phase_Fe3 to Fe3+ (Fe2O3) and Phase_Fetot to total iron (Fe2+ + Fe3+). For MAGEMin models and for Perple_X models calculated with O2 as a system component, Phase_Fe refers to total iron. Phase_Fe3 and Phase_Fetot must not be used in these cases, as the missing model values would exclude the whole phase from the calculation.
 
 **Row 2** provides observed compositional values in atoms per formula unit corresponding to each element specified in row 1.
 

{pyintersect-0.1.3 → pyintersect-0.1.4}/README.md

@@ -160,7 +160,7 @@ Measured mineral compositions must be provided in a tab-delimited text file. Com
 
 The file follows a specific six-row structure.
 
-**Row 1** specifies element identifiers using Phase_Element format where phase names follow Warr (2021) abbreviations. Consult mineral_symbols.toml to recognise abbreviations and their mappings.
+**Row 1** specifies element identifiers using Phase_Element format where phase names follow Warr (2021) abbreviations. Consult mineral_symbols.toml to recognise abbreviations and their mappings. Ferrous and ferric iron can be distinguished only for Perple_X models calculated with Fe2O3 as a system component. In this case, Phase_Fe refers to Fe2+ (FeO), Phase_Fe3 to Fe3+ (Fe2O3) and Phase_Fetot to total iron (Fe2+ + Fe3+). For MAGEMin models and for Perple_X models calculated with O2 as a system component, Phase_Fe refers to total iron. Phase_Fe3 and Phase_Fetot must not be used in these cases, as the missing model values would exclude the whole phase from the calculation.
 
 **Row 2** provides observed compositional values in atoms per formula unit corresponding to each element specified in row 1.
 

{pyintersect-0.1.3 → pyintersect-0.1.4}/docs/TECHNICAL.md

@@ -30,7 +30,7 @@ Compositional data in thermodynamic model outputs appears in oxide notation with
 
 Alternative patterns include bracket notation like Mg[apfu] and parenthetical notation such as Si(apfu). These typically indicate direct elemental abundances rather than oxide compositions and receive a coefficient of one. For ambiguous cases, the system extracts the first one or two characters as the element symbol with default coefficient of one.
 
-Element names are normalized through a lookup table handling common variations. This ensures sodium appears as Na rather than na, aluminum as Al rather than al, and similarly for other elements. Normalization operates independently of coefficient extraction, maintaining separation between identification of element presence and determination of stoichiometric contribution.
+Element names are normalized through a lookup table handling common variations. This ensures sodium appears as Na rather than na, aluminum as Al rather than al, and similarly for other elements. Normalization operates independently of coefficient extraction, maintaining separation between identification of element presence and determination of stoichiometric contribution. Ferric iron is treated separately in Perple_X outputs calculated with Fe2O3 as a system component. Columns in Fe2O3 notation are stored as Fe3. When both Fe and Fe3 are present, total iron is stored as Fetot and is used for endmember discrimination. MAGEMin outputs report total iron as Fe[apfu], and no separate Fe3 or Fetot values are created.
 
 ### Compositional Data Filtering
 

{pyintersect-0.1.3 → pyintersect-0.1.4}/docs/USER_GUIDE.md

@@ -56,6 +56,8 @@ The first row contains element identifiers combining phase names with element sy
 
 Example identifiers for a garnet-muscovite-biotite-plagioclase assemblage would include Grt_Mg, Grt_Fe, Grt_Ca, Grt_Mn, Ms_Si, Ms_Al, Ms_K, Ms_Mg, Bt_Mg, Bt_Fe, Bt_Si, Bt_K, Pl_Ca, Pl_Na, Pl_Al, Pl_Si. The specific elements chosen should reflect compositional variables that constrain pressure-temperature-composition conditions. Elements involved in substitutions in the solution models should be considered, depending on the selected chemical system, database and solution models.
 
+Iron requires particular attention, as the distinction between ferrous and ferric iron is available only for Perple_X models calculated with Fe2O3 as a system component. In this case, the model output contains separate FeO and Fe2O3 columns. Grt_Fe is compared with ferrous iron (FeO), Grt_Fe3 with ferric iron (Fe2O3) and Grt_Fetot with total iron (Fe2+ + Fe3+). Grt_Fetot should be used when the measured iron is not recalculated into Fe2+ and Fe3+ (e.g. EPMA analyses without charge-balance recalculation). Conversely, MAGEMin models ferric iron through the O component and reports total iron only. The same applies to Perple_X models calculated with O2 as a system component. In both cases, Grt_Fe is compared with total iron, and the measured value must therefore be total iron. Grt_Fe3 and Grt_Fetot must not be used, as the corresponding model values are missing and the whole phase would be excluded from the quality factor calculation.
+
 <p align="center">
   <img src="images/input_file_structure.png" alt="Annotated measured composition input file" width="650">
   <br>

pyintersect-0.1.4/example/CUSO-workshop-Lausanne-2026/BAR38A_coe_observed.txt

@@ -0,0 +1,11 @@
+# IntersecT tutorial
+# BAR38A sample from Petroccia et al. (2025) [Geochemistry, Geophysics, Geosystems, 26, e2025GC012412. https://doi.org/10.1029/2025GC012412] 
+# UHP metapelite, modelling garnet rim stability at HP-UHP
+
+Grt_Mg	Grt_Ca	Grt_Mn	Grt_Fe	Cld_Mg	Cld_Fe	Ms_Mg	Ms_Fe	Ms_Si	Ms_Al	Ms_Na	Coe_Si
+0.35	0.16	0.05	2.32	0.21	0.8	0.38	0.08	3.57	1.96	0.04	1.001
+0.09	0.07	0.02	0.69	0.05	0.08	0.09	0.04	0.21	0.21	0.04	0.001
+WDS map
+
+Colour scheme:
+viridis