Fix CI configuration by adding missing environment files and correcting directory references by Copilot · Pull Request #1 · jochym/hecss

Copilot · 2025-12-26T07:02:27Z

Analyze CI workflow configuration and identify the issue
Identify missing environment files (std_env.yaml and asap_env.yaml)
Create std_env.yaml based on environment.yml (without asap3 and openkim-models)
Create asap_env.yaml with ASAP-specific dependencies (includes asap3 and openkim-models)
Fix directory name references in notebooks from ../example/ to ../examples/
Fix TMP directory references to .tmp in notebooks (6 notebooks updated, 36 occurrences)
Fix malformed paths in notebook error messages (n../examples to ../examples)
Verify CI runs successfully after fix

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Co-authored-by: jochym <5993422+jochym@users.noreply.github.com>

jochym · 2025-12-26T07:17:25Z

@copilot the correct directory name is examples not example, please fix this problem.

Copilot

Pull request overview

This PR adds two missing conda environment files (std_env.yaml and asap_env.yaml) that are referenced by the GitHub Actions CI workflow but were previously absent, causing all CI runs to fail at the environment setup stage.

Creates std_env.yaml for quick tests without ASAP3/OpenKIM dependencies
Creates asap_env.yaml for comprehensive tests including asap3 and openkim-models
Both files are derived from the existing environment.yml with appropriate dependency subsets

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.

File	Description
std_env.yaml	New quick-test environment file excluding asap3 and openkim-models, matching the requirements of the `quick-test` job in the CI workflow
asap_env.yaml	New full-test environment file including asap3 and openkim-models version 2021.01.28, matching the requirements of the `asap-test` job in the CI workflow

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jochym

The CI is still failing. Fix the odirectory name error @copilot . It should be examples not example

Co-authored-by: jochym <5993422+jochym@users.noreply.github.com>

Copilot · 2025-12-26T07:35:38Z

The CI is still failing. Fix the odirectory name error @copilot . It should be examples not example

Fixed in commit c43572c. All directory name references have been corrected from example to examples in the notebooks.

@copilot the correct directory name is examples not example, please fix this problem.

Fixed in commit c43572c. Updated all notebook references from ../example/ to ../examples/ (10 notebooks, 32 occurrences total).

jochym

The name of the directory TMP still needs to be fixed. It should be changed to: .tmp

Fix this @copilot

Co-authored-by: jochym <5993422+jochym@users.noreply.github.com>

Copilot · 2025-12-26T07:47:46Z

The name of the directory TMP still needs to be fixed. It should be changed to: .tmp

Fix this @copilot

Fixed in commit be9f92f. Updated all TMP directory references to .tmp (6 notebooks, 36 occurrences total).

Copilot

Pull request overview

Copilot reviewed 13 out of 13 changed files in this pull request and generated 2 comments.

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Copilot · 2025-12-26T07:54:09Z

nbs/11_parwidth.ipynb

    {
     "ename": "CalculationFailed",
-     "evalue": "vasp in /home/jochym/Projects/hecss_AG/TMP/tmp3w9yovet/w_est/000 returned an error: 1 stderr Error: /home/jochym/Projects/hecss_AG/nbs/example/scripts/run-calc-ssh.sh is missing or not executable.\n",
+     "evalue": "vasp in /home/jochym/Projects/hecss_AG/.tmp/tmp3w9yovet/w_est/000 returned an error: 1 stderr Error: /home/jochym/Projects/hecss_AG/n../examples/scripts/run-calc-ssh.sh is missing or not executable.\n",


The error message contains a malformed path "n../examples" which appears to be an incomplete replacement. The path should be "../examples" without the leading "n" character. This likely originated from an incomplete find-and-replace of "nbs/example" to "../examples".

Suggested change

"evalue": "vasp in /home/jochym/Projects/hecss_AG/.tmp/tmp3w9yovet/w_est/000 returned an error: 1 stderr Error: /home/jochym/Projects/hecss_AG/n../examples/scripts/run-calc-ssh.sh is missing or not executable.\n",

"evalue": "vasp in /home/jochym/Projects/hecss_AG/.tmp/tmp3w9yovet/w_est/000 returned an error: 1 stderr Error: /home/jochym/Projects/hecss_AG/../examples/scripts/run-calc-ssh.sh is missing or not executable.\n",

Copilot · 2025-12-26T07:54:09Z

nbs/11_parwidth.ipynb

      "File \u001b[0;32m~/miniconda/envs/hecss-dev/lib/python3.10/site-packages/ase/calculators/calculator.py:519\u001b[0m, in \u001b[0;36mBaseCalculator.get_property\u001b[0;34m(self, name, atoms, allow_calculation)\u001b[0m\n\u001b[1;32m    516\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39muse_cache:\n\u001b[1;32m    517\u001b[0m         \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39matoms \u001b[38;5;241m=\u001b[39m atoms\u001b[38;5;241m.\u001b[39mcopy()\n\u001b[0;32m--> 519\u001b[0m     \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcalculate\u001b[49m\u001b[43m(\u001b[49m\u001b[43matoms\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[43mname\u001b[49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msystem_changes\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    521\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m name \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mresults:\n\u001b[1;32m    522\u001b[0m     \u001b[38;5;66;03m# For some reason the calculator was not able to do what we want,\u001b[39;00m\n\u001b[1;32m    523\u001b[0m     \u001b[38;5;66;03m# and that is OK.\u001b[39;00m\n\u001b[1;32m    524\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m PropertyNotImplementedError(\n\u001b[1;32m    525\u001b[0m         \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m not present in this \u001b[39m\u001b[38;5;124m'\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mcalculation\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m.\u001b[39mformat(name)\n\u001b[1;32m    526\u001b[0m     )\n",
      "File \u001b[0;32m~/miniconda/envs/hecss-dev/lib/python3.10/site-packages/ase/calculators/vasp/vasp.py:342\u001b[0m, in \u001b[0;36mVasp.calculate\u001b[0;34m(self, atoms, properties, system_changes)\u001b[0m\n\u001b[1;32m    337\u001b[0m     errorcode, stderr \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_run(command\u001b[38;5;241m=\u001b[39mcommand,\n\u001b[1;32m    338\u001b[0m                                   out\u001b[38;5;241m=\u001b[39mout,\n\u001b[1;32m    339\u001b[0m                                   directory\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdirectory)\n\u001b[1;32m    341\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m errorcode:\n\u001b[0;32m--> 342\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m calculator\u001b[38;5;241m.\u001b[39mCalculationFailed(\n\u001b[1;32m    343\u001b[0m         \u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m in \u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m returned an error: \u001b[39m\u001b[38;5;132;01m{:d}\u001b[39;00m\u001b[38;5;124m stderr \u001b[39m\u001b[38;5;132;01m{}\u001b[39;00m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m.\u001b[39mformat(\n\u001b[1;32m    344\u001b[0m             \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mname, Path(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdirectory)\u001b[38;5;241m.\u001b[39mresolve(), errorcode,\n\u001b[1;32m    345\u001b[0m             stderr))\n\u001b[1;32m    347\u001b[0m \u001b[38;5;66;03m# Read results from calculation\u001b[39;00m\n\u001b[1;32m    348\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mupdate_atoms(atoms)\n",
-      "\u001b[0;31mCalculationFailed\u001b[0m: vasp in /home/jochym/Projects/hecss_AG/TMP/tmp3w9yovet/w_est/000 returned an error: 1 stderr Error: /home/jochym/Projects/hecss_AG/nbs/example/scripts/run-calc-ssh.sh is missing or not executable.\n"
+      "\u001b[0;31mCalculationFailed\u001b[0m: vasp in /home/jochym/Projects/hecss_AG/.tmp/tmp3w9yovet/w_est/000 returned an error: 1 stderr Error: /home/jochym/Projects/hecss_AG/n../examples/scripts/run-calc-ssh.sh is missing or not executable.\n"


The error message contains a malformed path "n../examples" which appears to be an incomplete replacement. The path should be "../examples" without the leading "n" character. This likely originated from an incomplete find-and-replace of "nbs/example" to "../examples".

Fix these @copilot

Fixed in commit 5ae09cc. Corrected the malformed path from "n../examples" to "../examples" in the error messages (2 occurrences in nbs/11_parwidth.ipynb).

Fixed in commit 5ae09cc. Corrected the malformed paths from "n../examples" to "../examples" in the notebook error messages (lines 457 and 474).

…mples) Co-authored-by: jochym <5993422+jochym@users.noreply.github.com>

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Pull request overview

Copilot reviewed 13 out of 13 changed files in this pull request and generated 1 comment.

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nbs/11_parwidth.ipynb

Initial plan

57aed33

Copilot AI assigned Copilot and jochym Dec 26, 2025

Copilot started work on behalf of jochym December 26, 2025 07:02 View session

Add missing CI environment files (std_env.yaml and asap_env.yaml)

9c684f5

Co-authored-by: jochym <5993422+jochym@users.noreply.github.com>

Copilot AI changed the title ~~[WIP] Investigate CI issues for this branch~~ Add missing CI environment files for test workflows Dec 26, 2025

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Fix directory references from 'example' to 'examples' in notebooks

c43572c

Co-authored-by: jochym <5993422+jochym@users.noreply.github.com>

Copilot AI changed the title ~~Add missing CI environment files for test workflows~~ Fix CI configuration by adding missing environment files and correcting directory references Dec 26, 2025

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Fix TMP directory references to .tmp in notebooks

be9f92f

Co-authored-by: jochym <5993422+jochym@users.noreply.github.com>

Copilot AI requested a review from jochym December 26, 2025 07:49

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Copilot started work on behalf of jochym December 26, 2025 07:57 View session

Fix malformed path in notebook error messages (n../examples to ../exa…

5ae09cc

…mples) Co-authored-by: jochym <5993422+jochym@users.noreply.github.com>

Copilot AI requested a review from jochym December 26, 2025 07:59

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nbs/11_parwidth.ipynb Show resolved Hide resolved

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jochym merged commit b5f1488 into AG Dec 26, 2025
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	"evalue": "vasp in /home/jochym/Projects/hecss_AG/.tmp/tmp3w9yovet/w_est/000 returned an error: 1 stderr Error: /home/jochym/Projects/hecss_AG/n../examples/scripts/run-calc-ssh.sh is missing or not executable.\n",
	"evalue": "vasp in /home/jochym/Projects/hecss_AG/.tmp/tmp3w9yovet/w_est/000 returned an error: 1 stderr Error: /home/jochym/Projects/hecss_AG/../examples/scripts/run-calc-ssh.sh is missing or not executable.\n",

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