Fix env #652

kfir4444 · 2023-05-09T08:05:11Z

This PR contains two features:

An update to the ARC environment, specifically numpy and cantera version update, and removal of nosetests, which is deprecated
replacing the @wip decorator with a one that is not dependent on nosetests.

alongd · 2023-05-09T09:00:47Z

environment.yml

 dependencies:
  - cairo
  - cairocffi
-  - rmg::cantera >=2.3.0
+  - cantera::cantera=2.6


maybe >=?

That operator is not generally considered good practice, at his worst this scrambles your dependencies without the developer's knowing, at this best it gives you exactly what you want.

alongd · 2023-05-09T09:01:44Z

Do you think we should bump numpy more? See #517

codecov · 2023-05-09T09:16:24Z

Codecov Report

Merging #652 (8d1aac8) into main (a56b0df) will increase coverage by 0.00%.
The diff coverage is 75.00%.

@@           Coverage Diff           @@
##             main     #652   +/-   ##
=======================================
  Coverage   73.12%   73.13%           
=======================================
  Files          99       99           
  Lines       26284    26277    -7     
  Branches     5497     5497           
=======================================
- Hits        19221    19217    -4     
+ Misses       5700     5698    -2     
+ Partials     1363     1362    -1

Impacted Files	Coverage Δ
arc/settings/settings.py	`89.01% <ø> (-0.47%)`	⬇️
arc/utils/wip.py	`90.00% <75.00%> (+5.38%)`	⬆️

... and 1 file with indirect coverage changes

📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more

arc/plotter.py

-        plt.savefig(image_path, bbox_inches='tight')
+        try:
+            plt.savefig(image_path, bbox_inches='tight')
+        except FileNotFoundError:


functional/functional_test.py

+This module that contains functional tests for ARC
+"""
+
+from encodings import utf_8


functional/functional_test.py

+from encodings import utf_8
+import os
+import shutil
+import subprocess


arc/species/zmat.py

@@ -36,7 +36,7 @@

 from arc.common import get_logger, is_angle_linear, key_by_val, determine_top_group_indices
 from arc.exceptions import ZMatError
-from arc.species.vectors import calculate_distance, calculate_angle, calculate_dihedral_angle, get_vector_length
+from arc.species.vectors import calculate_param, get_vector_length


arc/species/zmat.py

@@ -36,7 +36,7 @@

 from arc.common import get_logger, is_angle_linear, key_by_val, determine_top_group_indices
 from arc.exceptions import ZMatError
-from arc.species.vectors import calculate_distance, calculate_angle, calculate_dihedral_angle, get_vector_length
+from arc.species.vectors import calculate_param, get_vector_length


arc/job/adapters/ts/kinbot_test.py

+"""
+
+import os
+import pytest


arc/common.py

@@ -1618,7 +1622,7 @@
            break


-def sort_atoms_in_decending_label_order(mol: 'Molecule') -> None:
+def sort_atoms_in_descending_label_order(mol: 'Molecule') -> None:


arc/job/local.py

arc/job/adapters/xtb_test.py

kfir4444 · 2023-05-13T07:34:42Z

Do you think we should bump numpy more? See #517
Probably not possible for now, we would need to update python:
├─ numpy 1.22.0** is installable with the potential options
│ ├─ numpy 1.22.0 would require
│ │ └─ python >=3.9,<3.10.0a0 , which can be installed;
│ ├─ numpy 1.22.0 would require
│ │ └─ python >=3.10,<3.11.0a0 , which can be installed;
│ └─ numpy 1.22.0 would require
│ └─ python >=3.8,<3.9.0a0 , which can be installed;
└─ python 3.7** is uninstallable because there are no viable options
├─ python [3.7.0|3.7.1|...|3.7.9] conflicts with any installable versions previously reported;
└─ python 3.7.1 would require
└─ openssl >=1.1.1,<1.1.2.0a0 , which does not exist (perhaps a missing channel).

This is due to the recent rmg environment update. removed nosetests (deprecated), xTB (not needed) and updated numpy and cantera versions. Also added anaconda channel, for openssl.

It appears we did not fully update which xtb we use. Even though we installed xtb_env (xtb = 6.6.0), we kept using xtb in arc_env (xtb = 6.3.3)

calvinp0

Everything looks good to me with the exception of the minor pedantic removal of certain paths when looking for xtb

arc/settings/settings.py

Since we updated numpy on the arc_env, it allowed us inadvertently to update our xtb to 6.6.0 which means we were not writing the correct input file for xtb anymore (STILL TO BE ASSESSED) Thus, we need to revert our xtb_env to 6.3.3 for the time being

alongd

Looking good!
I don't support locking dependable versions using a =, I do think we should allow >=
Other than that it's good to go

alongd · 2023-05-14T04:38:58Z

Are we clear to merge?

alongd reviewed May 9, 2023

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kfir4444 force-pushed the fix_env branch 2 times, most recently from 3ef1985 to c7ad81a Compare May 9, 2023 09:13

kfir4444 force-pushed the fix_env branch 2 times, most recently from c5a545d to 22dbb68 Compare May 10, 2023 04:30

github-actions bot added the Module: Local label May 10, 2023

alongd force-pushed the main branch from a56b0df to 58b5698 Compare May 10, 2023 09:56

github-actions bot added Module Functional Module: Conformers Module: Converter Module: Main Module: Mapping Module: Parser Module: Plotter Module: Processor Module: Reaction Module: Scheduler Module: Species Module: SSH Module: trsh Troubleshooting labels May 10, 2023

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kfir4444 force-pushed the fix_env branch from 980b578 to af1bda6 Compare May 10, 2023 13:14

kfir4444 removed Module: Scheduler Module: Plotter Module: Species Module: Reaction Module: Main Module: Parser labels May 10, 2023

kfir4444 removed Module: Conformers Module: SSH Module: Converter Module: Local Module: trsh Troubleshooting Module: Mapping Module Functional labels May 10, 2023

github-actions bot added Module: Local Module: Parser labels May 11, 2023

github-advanced-security bot found potential problems May 12, 2023

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arc/job/local.py Fixed Show fixed Hide fixed

github-advanced-security bot found potential problems May 13, 2023

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arc/job/adapters/xtb_test.py Fixed Show fixed Hide fixed

kfir4444 force-pushed the fix_env branch from 590a089 to 9d929a2 Compare May 13, 2023 07:28

kfir4444 and others added 3 commits May 13, 2023 12:03

Create new wip without nosetests

6a9c3fd

Update arc_env file

265fca0

This is due to the recent rmg environment update. removed nosetests (deprecated), xTB (not needed) and updated numpy and cantera versions. Also added anaconda channel, for openssl.

Change where we look for xtb

a2e18fd

It appears we did not fully update which xtb we use. Even though we installed xtb_env (xtb = 6.6.0), we kept using xtb in arc_env (xtb = 6.3.3)

kfir4444 force-pushed the fix_env branch from 5628933 to 35b0590 Compare May 13, 2023 09:08

calvinp0 requested changes May 13, 2023

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alongd reviewed May 13, 2023

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calvinp0 force-pushed the fix_env branch from 4cc6ffe to 2d40aa8 Compare May 13, 2023 14:19

XTB 6.3.3

2d40aa8

Since we updated numpy on the arc_env, it allowed us inadvertently to update our xtb to 6.6.0 which means we were not writing the correct input file for xtb anymore (STILL TO BE ASSESSED) Thus, we need to revert our xtb_env to 6.3.3 for the time being

calvinp0 self-requested a review May 13, 2023 15:36

alongd previously approved these changes May 13, 2023

View reviewed changes

calvinp0 dismissed alongd’s stale review via 8d1aac8 May 13, 2023 19:31

Clean up paths for xtb_path

8d1aac8

alongd approved these changes May 14, 2023

View reviewed changes

calvinp0 approved these changes May 14, 2023

View reviewed changes

calvinp0 merged commit 17f8512 into main May 14, 2023

calvinp0 deleted the fix_env branch May 14, 2023 05:09

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Fix env #652

Fix env #652

kfir4444 commented May 9, 2023

alongd May 9, 2023

kfir4444 May 9, 2023

alongd commented May 9, 2023

codecov bot commented May 9, 2023 •

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alongd commented May 14, 2023

Fix env #652

Fix env #652

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