Update the `main` with improvements done in `development` branch since the last paper #18

amkrajewski · 2025-08-22T15:00:23Z

A draft PR for @amr8004 to work on before we are ready to pull it and clean up the main afterwards

…sure correct results

…d some packages; conda-forge now

into development

… range methods

README updates from Main to Development

Copilot

Pull Request Overview

This PR merges improvements from the development branch into main since the last paper publication. The changes primarily focus on configuration refactoring, enhanced callable generation, and improved computational capabilities.

Key changes include:

Refactored YAML configuration structure from callables to elementalSpaces
Added hybrid Scheil-equilibrium simulation capabilities
Enhanced computational density settings and new utility functions

Reviewed Changes

Copilot reviewed 17 out of 29 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
testing_input.yaml	Removed old test configuration file
publication_input.yaml	Added comprehensive publication configuration with design spaces and stitching
import_yaml.py	New utility for parsing YAML configurations and generating component mappings
example_input.yaml	Added example configuration demonstrating multi-phase path planning
ammap/templates/hybrid_scheil_eq_callable_template.py	New template for hybrid Scheil-equilibrium calculations
ammap/templates/equilibrium_callable_template.py	Increased computational density from 2000 to 5000
ammap/callables/yaml_tools.py	New utility for updating feasible phases in YAML files
ammap/callables/plotting.py	New 3D graph plotting functionality using igraph and plotly
ammap/callableBuilders/hybrid_callables.py	New builder for hybrid callable generation
ammap/callableBuilders/construct_callables_combo.py	Enhanced callable builder supporting multiple constraint types
ammap/callableBuilders/construct_callables.py	Updated to use `elementalSpaces` instead of `callables`
UPDATE.txt	Documentation of changes to implement
Ti-Al-V-Cr.TDB	Added thermodynamic database for Ti-Al-V-Cr system
Old_demos_and_workshops/AMMapDemonstration.ipynb	Updated execution counts and added error handling
CONICRFE_input.yaml	New configuration for Co-Ni-Cr-Fe system analysis

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ammap/callableBuilders/construct_callables.py

ammap/callableBuilders/construct_callables_combo.py

Copilot · 2025-08-22T15:03:20Z

ammap/callableBuilders/hybrid_callables.py

+        Path(f"{output_dir}/__init__.py").touch()
+
+    # Read the hybrid Scheil-equilibrium template file
+    with open('ammap/templates/hybrid_scheil_eq_callable_template_perp.py', 'r') as f:


The file path 'hybrid_scheil_eq_callable_template_perp.py' does not match the actual template file 'hybrid_scheil_eq_callable_template.py' that was added to the repository. This will cause a FileNotFoundError.

Suggested change

with open('ammap/templates/hybrid_scheil_eq_callable_template_perp.py', 'r') as f:

with open('ammap/templates/hybrid_scheil_eq_callable_template.py', 'r') as f:

ammap/callables/yaml_tools.py

Copilot · 2025-08-22T15:03:21Z

import_yaml.py

+import re
+
+# Load the YAML file
+with open('example_input.yaml', 'r') as file:


The hardcoded filename 'example_input.yaml' should be parameterized to make the script reusable with different input files. Consider accepting the filename as a command-line argument or function parameter.

Suggested change

with open('example_input.yaml', 'r') as file:

import argparse

parser = argparse.ArgumentParser(description='Process a YAML file.')

parser.add_argument('filename', type=str, help='Path to the input YAML file')

args = parser.parse_args()

# Load the YAML file

with open(args.filename, 'r') as file:

ammap/templates/hybrid_scheil_eq_callable_template.py

amkrajewski

@amr8004 Please have a look at my comments

amkrajewski · 2025-08-22T15:02:44Z

CONICRFE_input.yaml

@amr8004 This probably should land in some examples or tutorial directory

amkrajewski · 2025-08-22T15:02:56Z

CoCrFeNi.ipynb

This probably should land in some examples or tutorial directory

amkrajewski · 2025-08-22T15:04:07Z

AMMap_publication_demonstration.ipynb

The publication demonstration can proably stay in root

amkrajewski · 2025-08-22T15:04:20Z

N-Dimensional-SingleTDB-full.ipynb

This probably should land in some examples or tutorial directory

amkrajewski · 2025-08-22T15:05:21Z

Old_demos_and_workshops/AMMapDemonstration.ipynb

Consider renamig the folder to proper snake case with lower-case o

amkrajewski · 2025-08-22T15:06:40Z

UPDATE.txt

Probably need to delete this one

amkrajewski · 2025-08-22T15:08:48Z

ammap/callables/yaml_tools.py

Docstrings need an overhaul in terms of what it does. Examples should also move to the docstring

amkrajewski · 2025-08-22T15:10:34Z

import_yaml.py

+# Combine all the names of each entry in designSpaces
+attainableSpaceComponents = []
+for entry in design_spaces:
+    components = re.findall(r'[A-Z][a-z]*', entry['name'])


This can probably be simplified

amkrajewski · 2025-08-22T15:11:26Z

publication_input.yaml

This belongs next to publication YAML for now, but probably should land in some examples or tutorial directory later

amkrajewski · 2025-08-22T15:13:49Z

ammap/callableBuilders/hybrid_callables.py

+        Path(f"{output_dir}/__init__.py").touch()
+
+    # Read the hybrid Scheil-equilibrium template file
+    with open('ammap/templates/hybrid_scheil_eq_callable_template_perp.py', 'r') as f:


amkrajewski · 2025-08-26T07:43:32Z

In the templates, you should change names of capitalized variables like 'Sfrac' or 'T_eq'. You can consider something like 'fracS' or 'eqT'. You can use capitalized constants

amkrajewski · 2025-08-26T07:46:08Z

Good progress overall 😃 Food for thought - we need to think about how to generalize populating the templates at some point, so that it is easy to do it with a substitution dictionary rather than hardcoding

amr8004

I believe this is ready to be the main branch now

amkrajewski · 2025-09-30T03:45:30Z

Hey @amr8004 - thanks for organizing everything 🚀 I had a quick look over the new structure and it generally looks good, but we need to still make it a bit more straightforward to approach by new users.

The files like AMMap_publication_demonstration.ipynb and corresponging publication_input.yaml make sense to be featured in the root directory for now, but they should be clearly organized and connected (one idea is to append somethig like 0_ to their names and refactoring the code to reflect that.
At some point, we need to follow a single file naming convention. We currently have a bumch of NamesLikeThis, like_this, or stuff-like-this.

amkrajewski · 2025-09-30T03:48:27Z

@amr8004 I will also run Copilot on this and it will probably give you a couple of items to address, since this PR is very sizable and changes half of the codebase, so I would be very surprised if there were no issues with some broken imports and deprecated references.

Copilot

Pull Request Overview

Copilot reviewed 22 out of 38 changed files in this pull request and generated 4 comments.

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ammap/callables/cracking.py

ammap/templates/equilibrium_callable_template.py

ammap/callableBuilders/construct_callables_combo.py

DemosAndWorkshops/AMMapDemonstration.ipynb

amr8004 and others added 9 commits April 14, 2025 16:52

Staging for initial hybrid-scheil implementation. Needs testing to en…

237cf09

…sure correct results

- fixed the Dockerfile relying on Anaconda for install which droppe…

9c30b01

…d some packages; conda-forge now

- added missing igraph dependency to the Dockerfile

7baec4c

Updated For Debo's System

3a1de7a

Merge branch 'development' of https://github.com/PhasesResearchLab/AMMap

a99a7b8

into development

v0.1 example 2025

2235182

Major updates to automation via core function and updated equilibrium…

bbc7f0c

… range methods

Cleaning some deprecated information out of easily confused locations.

62dc2a4

Merge pull request #17 from PhasesResearchLab/main

a18ecf3

README updates from Main to Development

amkrajewski requested review from Copilot and amr8004 August 22, 2025 15:00

amkrajewski assigned amkrajewski and amr8004 Aug 22, 2025

amkrajewski added the enhancement New feature or request label Aug 22, 2025

Copilot AI reviewed Aug 22, 2025

View reviewed changes

amr8004 added 3 commits August 22, 2025 15:10

Repository cleaning

d379c3f

Merge commit 'a18ecf39040d3aa8489f75919ab556dfd2d2c1f9' into development

7e5f0e1

Fix formatting of README header in deprecated files

239ae60

amkrajewski commented Aug 22, 2025

View reviewed changes

amr8004 added 3 commits August 25, 2025 21:50

functional hybrid scheil

3c03342

Merge commit '239ae608f5fb9cfad96739290a8aa1d0099f5b76' into development

5c8af39

slightly cleaner template for hybrid

48ef90b

amr8004 added 4 commits September 26, 2025 12:30

housekeeping

5e9b905

housekeeping 0.2

5478f42

housekeep 0.3

12463d3

Housekeep 0.4

67a4b4a

amr8004 reviewed Sep 29, 2025

View reviewed changes

amkrajewski requested a review from Copilot September 30, 2025 03:48

Copilot AI reviewed Sep 30, 2025

View reviewed changes

amkrajewski mentioned this pull request Sep 30, 2025

pycalphad update #11

Open

amkrajewski changed the title ~~[DRAFT] Update the main with improvements done in development branch since the last paper~~ Update the main with improvements done in development branch since the last paper Sep 30, 2025

copilot revisions

7bc3d5e

	with open('ammap/templates/hybrid_scheil_eq_callable_template_perp.py', 'r') as f:
	with open('ammap/templates/hybrid_scheil_eq_callable_template.py', 'r') as f:

-with open('example_input.yaml', 'r') as file:
+import argparse
+parser = argparse.ArgumentParser(description='Process a YAML file.')
+parser.add_argument('filename', type=str, help='Path to the input YAML file')
+args = parser.parse_args()
+# Load the YAML file
+with open(args.filename, 'r') as file:

Update the main with improvements done in development branch since the last paper #18

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Update the `main` with improvements done in `development` branch since the last paper #18

Update the `main` with improvements done in `development` branch since the last paper #18