4174 only read indats using the indat class by clmould · Pull Request #4523 · ukaea/PROCESS

clmould · 2026-08-13T16:21:25Z

Description

Moves validate_input to the InDat class and rename to check_obsolete_variables
parse_input_file no longer re-reads the file line by line and instead uses the data read in by InDat
Fix PLR1702 errors in these files

Checklist

I confirm that I have completed the following checks:

My changes follow the PROCESS style guide
I have justified any large differences in the regression tests caused by this pull request in the comments.
I have added new tests where appropriate for the changes I have made.
If I have had to change any existing unit or integration tests, I have justified this change in the pull request comments.
If I have made documentation changes, I have checked they render correctly.
I have added documentation for my change, if appropriate.

codecov-commenter · 2026-09-02T13:08:16Z

Codecov Report

❌ Patch coverage is 76.50602% with 39 lines in your changes missing coverage. Please review.
✅ Project coverage is 50.34%. Comparing base (0b69cfc) to head (3a44a01).

Files with missing lines	Patch %	Lines
process/core/io/in_dat/base.py	55.42%	37 Missing ⚠️
process/core/input.py	97.29%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4523      +/-   ##
==========================================
+ Coverage   50.26%   50.34%   +0.08%     
==========================================
  Files         181      181              
  Lines       30629    30604      -25     
==========================================
+ Hits        15395    15407      +12     
+ Misses      15234    15197      -37

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je-cook

First round, I think there will be a few subsequent reviews, its a lot to unpick!

je-cook

a few cleanup ones

je-cook · 2026-09-25T08:17:17Z

all of this goes to this one line

Suggested change

parameters[module][item] = {"value": data["i_process_run_mode"].get_value, "comment": f"{PROCESSRunMode(iop_val).description}"}

I've kept iop_val in for now to have PROCESSRunMode(iop_val).description, but I can remove that and instead directly use PROCESSRunMode(data["i_process_run_mode"].get_value).description if you'd prefer?

timothy-nunn

A couple more in addition to James.

timothy-nunn · 2026-09-25T08:35:30Z

+        if variable_name == "bounds":
+            boundl = {}
+            boundu = {}
+            for index, bounds_dict in info.value.items():
+                try:
+                    idx = int(index)
+                except ValueError as e:
+                    raise ProcessValidationError(
+                        "The bounds need to be of the form boundl/u(index) = value"
+                    ) from e
+                if "l" in bounds_dict:
+                    boundl[idx] = bounds_dict["l"]
+                if "u" in bounds_dict:
+                    boundu[idx] = bounds_dict["u"]
+            # TODO could change them into arrays here?
+
+            info_boundl = info
+            info_boundl.value = boundl
+            info_boundl.name = "boundl"
+            variables = set_on_datastructure(
+                variable_name="boundl",
+                info=info_boundl,
+                data_structure_obj=data_structure_obj,
+                variables=variables,
+            )

-        # matches (variable name, array index, value)
-        # NOTE: array index is Fortran-based hence starts at 1.
-        line_match = re.match(
-            r"([a-zA-Z0-9_]+)(?:\(([0-9]+)\))?[ ]*=[ ]*([ +\-a-zA-Z0-9.,]+).*",
-            stripped_line,
-        )
+            info_boundu = info
+            info_boundu.value = boundu
+            info_boundu.name = "boundu"


Could this be an additional action, rather than an if statement in the parser?

Have discussed and decided, for now, to add a new function _handle_bounds - the additional actions are not performed until after the variable validating and cleaning, which means it would be tricky to move this to an additional action and still be able to clean and validate the variable. Can always change once we have decided on how to handle bounds in future

…bles

…undl(index) = value , and use f_nd_impurity_electrons instead of bound in a test for input array remove outdated comment and add TODO docstring to fill in after review

… update any associated mfiles

…d updating

clmould linked an issue Aug 13, 2026 that may be closed by this pull request

Only read IN.DATs using the InDat class #4174

Open

1 of 2 tasks

clmould force-pushed the 4174-only-read-indats-using-the-indat-class branch from bc34539 to eda15dc Compare August 13, 2026 16:26

clmould mentioned this pull request Aug 14, 2026

Only read IN.DATs using the InDat class #4174

Open

1 of 2 tasks

clmould force-pushed the 4174-only-read-indats-using-the-indat-class branch 3 times, most recently from 72a627d to e8a494b Compare August 27, 2026 13:14

clmould force-pushed the 4174-only-read-indats-using-the-indat-class branch 6 times, most recently from 9816a42 to d4d920c Compare September 2, 2026 12:47

clmould force-pushed the 4174-only-read-indats-using-the-indat-class branch 2 times, most recently from 756ea41 to 698f4a5 Compare September 11, 2026 18:08

clmould force-pushed the 4174-only-read-indats-using-the-indat-class branch from fec93fb to bcd063a Compare September 21, 2026 12:27

clmould marked this pull request as ready for review September 22, 2026 14:06

clmould requested a review from a team as a code owner September 22, 2026 14:06

clmould assigned timothy-nunn and je-cook Sep 22, 2026

je-cook requested changes Sep 25, 2026

View reviewed changes

Comment thread process/core/io/in_dat/base.py Outdated

Comment thread process/core/io/in_dat/base.py Outdated

Comment thread process/core/io/in_dat/base.py Outdated

Comment thread process/core/input.py

je-cook reviewed Sep 25, 2026

View reviewed changes

timothy-nunn reviewed Sep 25, 2026

View reviewed changes

clmould added 7 commits October 23, 2026 17:39

move validate_input to InDat class and rename to check_obsolete_varia…

0506a1c

…bles

Fix test_main.py failures from moving obsolete var check to InDat class

971cd5d

check_process unused arg _inputs

13d5488

use fileprefix instead of output_prefix

05873b3

fix test

d831c2c

remove unused import

264ed3e

WIP parse_input_file is working

e9b960b

clmould added 15 commits October 23, 2026 17:39

fix failing tests - add error message if bounds aren't of the form bo…

0c2ede2

…undl(index) = value , and use f_nd_impurity_electrons instead of bound in a test for input array remove outdated comment and add TODO docstring to fill in after review

inform of duplicate variables and update these in our test files, and…

5658fed

… update any associated mfiles

remove refs to outdated vars impurity_radiation/imp_rad and vmec

424ca66

add missing docstring in input.py

7101d5c

remove unused line number in in_dat/base.py

1c15470

tidy up variable_constraint_type_check, sort evals, reword error msg

22a9e88

remove calls to unnecessary function

e4e0951

accidentally changed

b1184a0

undo mistake

8f42173

inputs , not _inputs

6fb1443

remove unnecessary code

f63d4ee

check obsolete in read_in_dat, split into smaller fns for checking an…

c85f92b

…d updating

james comments

3cd0760

create _handle_bounds fn

87ea23e

docstrign

d3d4bde

clmould force-pushed the 4174-only-read-indats-using-the-indat-class branch from c9765aa to 43c5333 Compare October 23, 2026 16:43

clmould added 2 commits October 23, 2026 18:46

fix pre-commit failure

ba45f43

remove duplicate vars from example data files

3a44a01

clmould marked this pull request as draft October 23, 2026 18:12

clmould force-pushed the 4174-only-read-indats-using-the-indat-class branch from cbd35eb to 3a44a01 Compare October 23, 2026 18:12


	parameters[module][item] = {"value": data["i_process_run_mode"].get_value, "comment": f"{PROCESSRunMode(iop_val).description}"}

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clmould commented Aug 13, 2026 •

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