﻿2026-01-05T01:33:08.3029647Z Current runner version: '2.330.0'
2026-01-05T01:33:08.3056352Z ##[group]Runner Image Provisioner
2026-01-05T01:33:08.3057225Z Hosted Compute Agent
2026-01-05T01:33:08.3057893Z Version: 20251211.462
2026-01-05T01:33:08.3058527Z Commit: 6cbad8c2bb55d58165063d031ccabf57e2d2db61
2026-01-05T01:33:08.3059249Z Build Date: 2025-12-11T16:28:49Z
2026-01-05T01:33:08.3060024Z Worker ID: {bc9fa132-3911-4fee-a78e-43844c702c19}
2026-01-05T01:33:08.3061125Z ##[endgroup]
2026-01-05T01:33:08.3061854Z ##[group]Operating System
2026-01-05T01:33:08.3062793Z Ubuntu
2026-01-05T01:33:08.3063423Z 24.04.3
2026-01-05T01:33:08.3064085Z LTS
2026-01-05T01:33:08.3064843Z ##[endgroup]
2026-01-05T01:33:08.3065623Z ##[group]Runner Image
2026-01-05T01:33:08.3066646Z Image: ubuntu-24.04
2026-01-05T01:33:08.3067446Z Version: 20251215.174.1
2026-01-05T01:33:08.3069051Z Included Software: https://github.com/actions/runner-images/blob/ubuntu24/20251215.174/images/ubuntu/Ubuntu2404-Readme.md
2026-01-05T01:33:08.3071548Z Image Release: https://github.com/actions/runner-images/releases/tag/ubuntu24%2F20251215.174
2026-01-05T01:33:08.3073243Z ##[endgroup]
2026-01-05T01:33:08.3077684Z ##[group]GITHUB_TOKEN Permissions
2026-01-05T01:33:08.3080739Z Actions: write
2026-01-05T01:33:08.3081653Z ArtifactMetadata: write
2026-01-05T01:33:08.3082786Z Attestations: write
2026-01-05T01:33:08.3083667Z Checks: write
2026-01-05T01:33:08.3084542Z Contents: write
2026-01-05T01:33:08.3085312Z Deployments: write
2026-01-05T01:33:08.3086627Z Discussions: write
2026-01-05T01:33:08.3087441Z Issues: write
2026-01-05T01:33:08.3088331Z Metadata: read
2026-01-05T01:33:08.3089282Z Models: read
2026-01-05T01:33:08.3090099Z Packages: write
2026-01-05T01:33:08.3090870Z Pages: write
2026-01-05T01:33:08.3091832Z PullRequests: write
2026-01-05T01:33:08.3092768Z RepositoryProjects: write
2026-01-05T01:33:08.3093652Z SecurityEvents: write
2026-01-05T01:33:08.3094616Z Statuses: write
2026-01-05T01:33:08.3095362Z ##[endgroup]
2026-01-05T01:33:08.3099495Z Secret source: Actions
2026-01-05T01:33:08.3100781Z Prepare workflow directory
2026-01-05T01:33:08.3587617Z Prepare all required actions
2026-01-05T01:33:08.3645861Z Getting action download info
2026-01-05T01:33:08.6899992Z Download action repository 'actions/checkout@v4' (SHA:34e114876b0b11c390a56381ad16ebd13914f8d5)
2026-01-05T01:33:08.7927784Z Download action repository 'actions/setup-python@v5' (SHA:a26af69be951a213d495a4c3e4e4022e16d87065)
2026-01-05T01:33:08.8864567Z Download action repository 'actions/download-artifact@v4' (SHA:d3f86a106a0bac45b974a628896c90dbdf5c8093)
2026-01-05T01:33:09.5642279Z Complete job name: Test wheels on ubuntu-latest with Python 3.13
2026-01-05T01:33:09.6461246Z ##[group]Run actions/checkout@v4
2026-01-05T01:33:09.6462766Z with:
2026-01-05T01:33:09.6463552Z   repository: worm-portal/aqequil
2026-01-05T01:33:09.6464886Z   token: ***
2026-01-05T01:33:09.6465618Z   ssh-strict: true
2026-01-05T01:33:09.6466652Z   ssh-user: git
2026-01-05T01:33:09.6467446Z   persist-credentials: true
2026-01-05T01:33:09.6468328Z   clean: true
2026-01-05T01:33:09.6469168Z   sparse-checkout-cone-mode: true
2026-01-05T01:33:09.6470126Z   fetch-depth: 1
2026-01-05T01:33:09.6470880Z   fetch-tags: false
2026-01-05T01:33:09.6471672Z   show-progress: true
2026-01-05T01:33:09.6472465Z   lfs: false
2026-01-05T01:33:09.6473180Z   submodules: false
2026-01-05T01:33:09.6473962Z   set-safe-directory: true
2026-01-05T01:33:09.6475188Z ##[endgroup]
2026-01-05T01:33:09.7623922Z Syncing repository: worm-portal/aqequil
2026-01-05T01:33:09.7627418Z ##[group]Getting Git version info
2026-01-05T01:33:09.7628766Z Working directory is '/home/runner/work/aqequil/aqequil'
2026-01-05T01:33:09.7630747Z [command]/usr/bin/git version
2026-01-05T01:33:09.7708136Z git version 2.52.0
2026-01-05T01:33:09.7739311Z ##[endgroup]
2026-01-05T01:33:09.7755112Z Temporarily overriding HOME='/home/runner/work/_temp/c9c2324f-8bab-4107-b912-dc2ee52d54d2' before making global git config changes
2026-01-05T01:33:09.7768597Z Adding repository directory to the temporary git global config as a safe directory
2026-01-05T01:33:09.7771210Z [command]/usr/bin/git config --global --add safe.directory /home/runner/work/aqequil/aqequil
2026-01-05T01:33:09.7814884Z Deleting the contents of '/home/runner/work/aqequil/aqequil'
2026-01-05T01:33:09.7819468Z ##[group]Initializing the repository
2026-01-05T01:33:09.7823652Z [command]/usr/bin/git init /home/runner/work/aqequil/aqequil
2026-01-05T01:33:09.7940653Z hint: Using 'master' as the name for the initial branch. This default branch name
2026-01-05T01:33:09.7943978Z hint: will change to "main" in Git 3.0. To configure the initial branch name
2026-01-05T01:33:09.7947405Z hint: to use in all of your new repositories, which will suppress this warning,
2026-01-05T01:33:09.7949260Z hint: call:
2026-01-05T01:33:09.7949955Z hint:
2026-01-05T01:33:09.7950891Z hint: 	git config --global init.defaultBranch <name>
2026-01-05T01:33:09.7952039Z hint:
2026-01-05T01:33:09.7953294Z hint: Names commonly chosen instead of 'master' are 'main', 'trunk' and
2026-01-05T01:33:09.7955613Z hint: 'development'. The just-created branch can be renamed via this command:
2026-01-05T01:33:09.7957644Z hint:
2026-01-05T01:33:09.7958563Z hint: 	git branch -m <name>
2026-01-05T01:33:09.7959420Z hint:
2026-01-05T01:33:09.7961074Z hint: Disable this message with "git config set advice.defaultBranchName false"
2026-01-05T01:33:09.7963086Z Initialized empty Git repository in /home/runner/work/aqequil/aqequil/.git/
2026-01-05T01:33:09.7966508Z [command]/usr/bin/git remote add origin https://github.com/worm-portal/aqequil
2026-01-05T01:33:09.8003702Z ##[endgroup]
2026-01-05T01:33:09.8005208Z ##[group]Disabling automatic garbage collection
2026-01-05T01:33:09.8007049Z [command]/usr/bin/git config --local gc.auto 0
2026-01-05T01:33:09.8041495Z ##[endgroup]
2026-01-05T01:33:09.8042933Z ##[group]Setting up auth
2026-01-05T01:33:09.8047741Z [command]/usr/bin/git config --local --name-only --get-regexp core\.sshCommand
2026-01-05T01:33:09.8082538Z [command]/usr/bin/git submodule foreach --recursive sh -c "git config --local --name-only --get-regexp 'core\.sshCommand' && git config --local --unset-all 'core.sshCommand' || :"
2026-01-05T01:33:09.8480121Z [command]/usr/bin/git config --local --name-only --get-regexp http\.https\:\/\/github\.com\/\.extraheader
2026-01-05T01:33:09.8515482Z [command]/usr/bin/git submodule foreach --recursive sh -c "git config --local --name-only --get-regexp 'http\.https\:\/\/github\.com\/\.extraheader' && git config --local --unset-all 'http.https://github.com/.extraheader' || :"
2026-01-05T01:33:09.8754817Z [command]/usr/bin/git config --local --name-only --get-regexp ^includeIf\.gitdir:
2026-01-05T01:33:09.8792935Z [command]/usr/bin/git submodule foreach --recursive git config --local --show-origin --name-only --get-regexp remote.origin.url
2026-01-05T01:33:09.9045895Z [command]/usr/bin/git config --local http.https://github.com/.extraheader AUTHORIZATION: basic ***
2026-01-05T01:33:09.9085543Z ##[endgroup]
2026-01-05T01:33:09.9087478Z ##[group]Fetching the repository
2026-01-05T01:33:09.9094756Z [command]/usr/bin/git -c protocol.version=2 fetch --no-tags --prune --no-recurse-submodules --depth=1 origin +0fba8641708a9a29f5cf75d5e1aa5af56402a902:refs/tags/v1.0.1
2026-01-05T01:33:10.3723326Z From https://github.com/worm-portal/aqequil
2026-01-05T01:33:10.3725581Z  * [new ref]         0fba8641708a9a29f5cf75d5e1aa5af56402a902 -> v1.0.1
2026-01-05T01:33:10.3755681Z ##[endgroup]
2026-01-05T01:33:10.3758009Z ##[group]Determining the checkout info
2026-01-05T01:33:10.3759729Z ##[endgroup]
2026-01-05T01:33:10.3762411Z [command]/usr/bin/git sparse-checkout disable
2026-01-05T01:33:10.3806445Z [command]/usr/bin/git config --local --unset-all extensions.worktreeConfig
2026-01-05T01:33:10.3833922Z ##[group]Checking out the ref
2026-01-05T01:33:10.3837637Z [command]/usr/bin/git checkout --progress --force refs/tags/v1.0.1
2026-01-05T01:33:10.4787370Z Note: switching to 'refs/tags/v1.0.1'.
2026-01-05T01:33:10.4788680Z 
2026-01-05T01:33:10.4789781Z You are in 'detached HEAD' state. You can look around, make experimental
2026-01-05T01:33:10.4793093Z changes and commit them, and you can discard any commits you make in this
2026-01-05T01:33:10.4795040Z state without impacting any branches by switching back to a branch.
2026-01-05T01:33:10.4796311Z 
2026-01-05T01:33:10.4796986Z If you want to create a new branch to retain commits you create, you may
2026-01-05T01:33:10.4798688Z do so (now or later) by using -c with the switch command. Example:
2026-01-05T01:33:10.4800091Z 
2026-01-05T01:33:10.4800466Z   git switch -c <new-branch-name>
2026-01-05T01:33:10.4801094Z 
2026-01-05T01:33:10.4801431Z Or undo this operation with:
2026-01-05T01:33:10.4802023Z 
2026-01-05T01:33:10.4802344Z   git switch -
2026-01-05T01:33:10.4802795Z 
2026-01-05T01:33:10.4803717Z Turn off this advice by setting config variable advice.detachedHead to false
2026-01-05T01:33:10.4805039Z 
2026-01-05T01:33:10.4805864Z HEAD is now at 0fba864 Add automatic versioning from git tags using setuptools_scm
2026-01-05T01:33:10.4809335Z ##[endgroup]
2026-01-05T01:33:10.4846623Z [command]/usr/bin/git log -1 --format=%H
2026-01-05T01:33:10.4875844Z 0fba8641708a9a29f5cf75d5e1aa5af56402a902
2026-01-05T01:33:10.5223403Z ##[group]Run actions/setup-python@v5
2026-01-05T01:33:10.5224485Z with:
2026-01-05T01:33:10.5225487Z   python-version: 3.13
2026-01-05T01:33:10.5226755Z   check-latest: false
2026-01-05T01:33:10.5227851Z   token: ***
2026-01-05T01:33:10.5228558Z   update-environment: true
2026-01-05T01:33:10.5229417Z   allow-prereleases: false
2026-01-05T01:33:10.5230395Z   freethreaded: false
2026-01-05T01:33:10.5231254Z ##[endgroup]
2026-01-05T01:33:10.7005405Z ##[group]Installed versions
2026-01-05T01:33:10.7131944Z Successfully set up CPython (3.13.11)
2026-01-05T01:33:10.7134885Z ##[endgroup]
2026-01-05T01:33:10.7333460Z ##[group]Run actions/download-artifact@v4
2026-01-05T01:33:10.7334471Z with:
2026-01-05T01:33:10.7335141Z   name: wheels-ubuntu-latest
2026-01-05T01:33:10.7335985Z   path: wheelhouse
2026-01-05T01:33:10.7336874Z   merge-multiple: false
2026-01-05T01:33:10.7337717Z   repository: worm-portal/aqequil
2026-01-05T01:33:10.7338612Z   run-id: 20702070857
2026-01-05T01:33:10.7339321Z env:
2026-01-05T01:33:10.7340177Z   pythonLocation: /opt/hostedtoolcache/Python/3.13.11/x64
2026-01-05T01:33:10.7341707Z   PKG_CONFIG_PATH: /opt/hostedtoolcache/Python/3.13.11/x64/lib/pkgconfig
2026-01-05T01:33:10.7343224Z   Python_ROOT_DIR: /opt/hostedtoolcache/Python/3.13.11/x64
2026-01-05T01:33:10.7344572Z   Python2_ROOT_DIR: /opt/hostedtoolcache/Python/3.13.11/x64
2026-01-05T01:33:10.7345945Z   Python3_ROOT_DIR: /opt/hostedtoolcache/Python/3.13.11/x64
2026-01-05T01:33:10.7347485Z   LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.13.11/x64/lib
2026-01-05T01:33:10.7348627Z ##[endgroup]
2026-01-05T01:33:10.9579977Z Downloading single artifact
2026-01-05T01:33:11.0949220Z Preparing to download the following artifacts:
2026-01-05T01:33:11.0950771Z - wheels-ubuntu-latest (ID: 5019911133, Size: 24825482, Expected Digest: sha256:a6d43ff313b13b3a568b82ecd8c330433356ae553a4f11dccf013c81efd55f84)
2026-01-05T01:33:11.2128092Z Redirecting to blob download url: https://productionresultssa18.blob.core.windows.net/actions-results/26a74c06-72e1-4403-8f14-91bf0d49fcbc/workflow-job-run-10b32453-0282-5d43-9cab-5c3accd2aafc/artifacts/2d6b53937ef398bfc8399b6b7ef6373c2af7892c0717a43682f51187fe1997a9.zip
2026-01-05T01:33:11.2129724Z Starting download of artifact to: /home/runner/work/aqequil/aqequil/wheelhouse
2026-01-05T01:33:11.3506862Z (node:2117) [DEP0005] DeprecationWarning: Buffer() is deprecated due to security and usability issues. Please use the Buffer.alloc(), Buffer.allocUnsafe(), or Buffer.from() methods instead.
2026-01-05T01:33:11.3509046Z (Use `node --trace-deprecation ...` to show where the warning was created)
2026-01-05T01:33:12.0407612Z SHA256 digest of downloaded artifact is a6d43ff313b13b3a568b82ecd8c330433356ae553a4f11dccf013c81efd55f84
2026-01-05T01:33:12.0408872Z Artifact download completed successfully.
2026-01-05T01:33:12.0409438Z Total of 1 artifact(s) downloaded
2026-01-05T01:33:12.0415033Z Download artifact has finished successfully
2026-01-05T01:33:12.0558910Z ##[group]Run PYVER=$(echo "3.13" | tr -d '.')
2026-01-05T01:33:12.0559366Z [36;1mPYVER=$(echo "3.13" | tr -d '.')[0m
2026-01-05T01:33:12.0559762Z [36;1mpython -m pip install wheelhouse/aqequil-*-cp${PYVER}-*.whl[0m
2026-01-05T01:33:12.0608708Z shell: /usr/bin/bash --noprofile --norc -e -o pipefail {0}
2026-01-05T01:33:12.0609087Z env:
2026-01-05T01:33:12.0609378Z   pythonLocation: /opt/hostedtoolcache/Python/3.13.11/x64
2026-01-05T01:33:12.0609825Z   PKG_CONFIG_PATH: /opt/hostedtoolcache/Python/3.13.11/x64/lib/pkgconfig
2026-01-05T01:33:12.0610274Z   Python_ROOT_DIR: /opt/hostedtoolcache/Python/3.13.11/x64
2026-01-05T01:33:12.0610684Z   Python2_ROOT_DIR: /opt/hostedtoolcache/Python/3.13.11/x64
2026-01-05T01:33:12.0611083Z   Python3_ROOT_DIR: /opt/hostedtoolcache/Python/3.13.11/x64
2026-01-05T01:33:12.0611476Z   LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.13.11/x64/lib
2026-01-05T01:33:12.0611807Z ##[endgroup]
2026-01-05T01:33:14.0679190Z Processing ./wheelhouse/aqequil-1.0.2.dev0+g0fba86417.d20260105-cp313-cp313-manylinux_2_28_x86_64.whl
2026-01-05T01:33:14.2913019Z Collecting pandas (from aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:14.3495053Z   Downloading pandas-2.3.3-cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (91 kB)
2026-01-05T01:33:14.6012950Z Collecting numpy (from aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:14.6061014Z   Downloading numpy-2.4.0-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (6.6 kB)
2026-01-05T01:33:14.7454154Z Collecting matplotlib (from aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:14.7521778Z   Downloading matplotlib-3.10.8-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (52 kB)
2026-01-05T01:33:14.8102105Z Collecting plotly (from aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:14.8143186Z   Downloading plotly-6.5.0-py3-none-any.whl.metadata (8.5 kB)
2026-01-05T01:33:14.8641873Z Collecting ipython (from aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:14.8687123Z   Downloading ipython-9.8.0-py3-none-any.whl.metadata (4.5 kB)
2026-01-05T01:33:14.8867995Z Collecting chemparse (from aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:14.8946537Z   Downloading chemparse-0.3.2-py3-none-any.whl.metadata (1.7 kB)
2026-01-05T01:33:14.9090124Z Collecting dill (from aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:14.9129510Z   Downloading dill-0.4.0-py3-none-any.whl.metadata (10 kB)
2026-01-05T01:33:14.9264346Z Collecting periodictable (from aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:14.9394348Z   Downloading periodictable-2.0.2-py3-none-any.whl.metadata (5.4 kB)
2026-01-05T01:33:14.9613241Z Collecting natsort (from aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:14.9653336Z   Downloading natsort-8.4.0-py3-none-any.whl.metadata (21 kB)
2026-01-05T01:33:14.9785430Z Collecting roman (from aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:14.9834546Z   Downloading roman-5.2-py3-none-any.whl.metadata (4.3 kB)
2026-01-05T01:33:15.0192020Z Collecting ipywidgets (from aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:15.0240015Z   Downloading ipywidgets-8.1.8-py3-none-any.whl.metadata (2.4 kB)
2026-01-05T01:33:15.0417181Z Collecting wormutils (from aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:15.0481136Z   Downloading wormutils-0.2.0-py3-none-any.whl.metadata (723 bytes)
2026-01-05T01:33:15.0799326Z Collecting pychnosz (from aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:15.2231124Z   Downloading pychnosz-1.1.12-cp313-cp313-manylinux_2_28_x86_64.whl.metadata (8.2 kB)
2026-01-05T01:33:15.2447028Z Collecting decorator>=4.3.2 (from ipython->aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:15.2485010Z   Downloading decorator-5.2.1-py3-none-any.whl.metadata (3.9 kB)
2026-01-05T01:33:15.2595321Z Collecting ipython-pygments-lexers>=1.0.0 (from ipython->aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:15.2673986Z   Downloading ipython_pygments_lexers-1.1.1-py3-none-any.whl.metadata (1.1 kB)
2026-01-05T01:33:15.2824955Z Collecting jedi>=0.18.1 (from ipython->aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:15.2861011Z   Downloading jedi-0.19.2-py2.py3-none-any.whl.metadata (22 kB)
2026-01-05T01:33:15.3061738Z Collecting matplotlib-inline>=0.1.5 (from ipython->aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:15.3102837Z   Downloading matplotlib_inline-0.2.1-py3-none-any.whl.metadata (2.3 kB)
2026-01-05T01:33:15.3240865Z Collecting pexpect>4.3 (from ipython->aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:15.3275858Z   Downloading pexpect-4.9.0-py2.py3-none-any.whl.metadata (2.5 kB)
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2026-01-05T01:33:19.7131980Z Downloading idna-3.11-py3-none-any.whl (71 kB)
2026-01-05T01:33:19.7205588Z Downloading urllib3-2.6.2-py3-none-any.whl (131 kB)
2026-01-05T01:33:19.7284412Z Downloading certifi-2026.1.4-py3-none-any.whl (152 kB)
2026-01-05T01:33:20.0616425Z Installing collected packages: pytz, pure-eval, ptyprocess, widgetsnbextension, wcwidth, urllib3, tzdata, traitlets, six, roman, pyparsing, pygments, pillow, pexpect, parso, packaging, numpy, natsort, narwhals, kiwisolver, jupyterlab_widgets, importlib_resources, idna, fonttools, executing, dill, decorator, cycler, comm, chemparse, charset_normalizer, certifi, asttokens, stack_data, scipy, requests, python-dateutil, prompt_toolkit, plotly, periodictable, matplotlib-inline, jedi, ipython-pygments-lexers, contourpy, pandas, matplotlib, ipython, wormutils, pychnosz, ipywidgets, aqequil
2026-01-05T01:33:40.8394910Z 
2026-01-05T01:33:40.8460416Z Successfully installed aqequil-1.0.2.dev0+g0fba86417.d20260105 asttokens-3.0.1 certifi-2026.1.4 charset_normalizer-3.4.4 chemparse-0.3.2 comm-0.2.3 contourpy-1.3.3 cycler-0.12.1 decorator-5.2.1 dill-0.4.0 executing-2.2.1 fonttools-4.61.1 idna-3.11 importlib_resources-6.5.2 ipython-9.8.0 ipython-pygments-lexers-1.1.1 ipywidgets-8.1.8 jedi-0.19.2 jupyterlab_widgets-3.0.16 kiwisolver-1.4.9 matplotlib-3.10.8 matplotlib-inline-0.2.1 narwhals-2.14.0 natsort-8.4.0 numpy-2.4.0 packaging-25.0 pandas-2.3.3 parso-0.8.5 periodictable-2.0.2 pexpect-4.9.0 pillow-12.1.0 plotly-6.5.0 prompt_toolkit-3.0.52 ptyprocess-0.7.0 pure-eval-0.2.3 pychnosz-1.1.12 pygments-2.19.2 pyparsing-3.3.1 python-dateutil-2.9.0.post0 pytz-2025.2 requests-2.32.5 roman-5.2 scipy-1.16.3 six-1.17.0 stack_data-0.6.3 traitlets-5.14.3 tzdata-2025.3 urllib3-2.6.2 wcwidth-0.2.14 widgetsnbextension-4.0.15 wormutils-0.2.0
2026-01-05T01:33:41.2790159Z ##[group]Run cp "$GITHUB_WORKSPACE/test_integration.py" "$RUNNER_TEMP/"
2026-01-05T01:33:41.2790703Z [36;1mcp "$GITHUB_WORKSPACE/test_integration.py" "$RUNNER_TEMP/"[0m
2026-01-05T01:33:41.2791058Z [36;1mcd "$RUNNER_TEMP"[0m
2026-01-05T01:33:41.2791292Z [36;1mpython test_integration.py[0m
2026-01-05T01:33:41.2824971Z shell: /usr/bin/bash --noprofile --norc -e -o pipefail {0}
2026-01-05T01:33:41.2825301Z env:
2026-01-05T01:33:41.2825560Z   pythonLocation: /opt/hostedtoolcache/Python/3.13.11/x64
2026-01-05T01:33:41.2825998Z   PKG_CONFIG_PATH: /opt/hostedtoolcache/Python/3.13.11/x64/lib/pkgconfig
2026-01-05T01:33:41.2826763Z   Python_ROOT_DIR: /opt/hostedtoolcache/Python/3.13.11/x64
2026-01-05T01:33:41.2827133Z   Python2_ROOT_DIR: /opt/hostedtoolcache/Python/3.13.11/x64
2026-01-05T01:33:41.2827508Z   Python3_ROOT_DIR: /opt/hostedtoolcache/Python/3.13.11/x64
2026-01-05T01:33:41.2827913Z   LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.13.11/x64/lib
2026-01-05T01:33:41.2828257Z ##[endgroup]
2026-01-05T01:34:12.1963273Z 
2026-01-05T01:34:12.1963743Z ============================================================
2026-01-05T01:34:12.1964253Z AQEQUIL INTEGRATION TEST SUITE
2026-01-05T01:34:12.1964688Z ============================================================
2026-01-05T01:34:12.1964998Z Python: 3.13.11
2026-01-05T01:34:12.1967532Z Platform: linux
2026-01-05T01:34:12.1967867Z Architecture: x86_64
2026-01-05T01:34:12.1968235Z ============================================================
2026-01-05T01:34:12.1968666Z ============================================================
2026-01-05T01:34:12.1969183Z Test 1: Checking for bundled EQ3/6 executables
2026-01-05T01:34:12.1969612Z ============================================================
2026-01-05T01:34:12.1970395Z [OK] Found bundled executables at: /opt/hostedtoolcache/Python/3.13.11/x64/lib/python3.13/site-packages/aqequil/bin
2026-01-05T01:34:12.1971151Z   [OK] eq3nr (1.04 MB)
2026-01-05T01:34:12.1971448Z   [OK] eq6 (1.76 MB)
2026-01-05T01:34:12.1971744Z   [OK] eqpt (0.62 MB)
2026-01-05T01:34:12.1971929Z 
2026-01-05T01:34:12.1972066Z ============================================================
2026-01-05T01:34:12.1972504Z Test 2: Testing aqequil import and basic usage
2026-01-05T01:34:12.1972933Z ============================================================
2026-01-05T01:34:12.1973340Z [OK] Successfully imported aqequil
2026-01-05T01:34:12.1974165Z [OK] Found test data at: /opt/hostedtoolcache/Python/3.13.11/x64/lib/python3.13/site-packages/aqequil/test_data/input_example_wrm.csv
2026-01-05T01:34:12.1974871Z 
2026-01-05T01:34:12.1975016Z ============================================================
2026-01-05T01:34:12.1975486Z Test 3: Downloading latest data0.wrm from WORM-db
2026-01-05T01:34:12.1975909Z ============================================================
2026-01-05T01:34:12.1976850Z Downloading data0.wrm from https://raw.githubusercontent.com/worm-portal/WORM-db/master/data0.wrm...
2026-01-05T01:34:12.1977633Z [OK] Downloaded data0.wrm (573.8 KB)
2026-01-05T01:34:12.1978066Z [OK] Copied data0.wrm to test_data (replaced existing)
2026-01-05T01:34:12.1978558Z [OK] Copied data0.wrm to databases (replaced existing)
2026-01-05T01:34:12.1978880Z 
2026-01-05T01:34:12.1979031Z ============================================================
2026-01-05T01:34:12.1979483Z Test 4: Testing runeqpt (data0 to data1 conversion)
2026-01-05T01:34:12.1979921Z ============================================================
2026-01-05T01:34:12.1980366Z [INFO] Working directory: /tmp/tmp4jdz_k4v
2026-01-05T01:34:12.1980773Z [OK] Copied data0.wrm to working directory
2026-01-05T01:34:12.1981579Z Running EQPT on data0.wrm...
2026-01-05T01:34:12.1981901Z [OK] EQPT completed
2026-01-05T01:34:12.1982191Z [OK] data1.wrm created (0.36 MB)
2026-01-05T01:34:12.1982641Z [OK] Copied data1.wrm to bundled databases (replaced existing)
2026-01-05T01:34:12.1982993Z 
2026-01-05T01:34:12.1983133Z ============================================================
2026-01-05T01:34:12.1983878Z Test 5: Testing simple speciation (wrm database)
2026-01-05T01:34:12.1984320Z ============================================================
2026-01-05T01:34:12.1985167Z Running speciation on /opt/hostedtoolcache/Python/3.13.11/x64/lib/python3.13/site-packages/aqequil/test_data/input_example_wrm.csv...
2026-01-05T01:34:12.1986220Z [INFO] Working directory: /tmp/tmp1s776jdy
2026-01-05T01:34:12.1986655Z [OK] Copied data0.wrm to working directory
2026-01-05T01:34:12.1987075Z Running EQPT to create data1.wrm...
2026-01-05T01:34:12.1987469Z [OK] EQPT completed, data1.wrm created
2026-01-05T01:34:12.1987911Z [OK] AqEquil instance created with wrm database
2026-01-05T01:34:12.1988823Z The input file column 'logfO2' will be used to set sample redox state. If a another column is desired, set it manually using the redox_flag parameter.
2026-01-05T01:34:12.1989985Z No 'charge_balance_on' column found in input file. Defaulting to no charge balancing for all samples.
2026-01-05T01:34:12.1991110Z Warning: no 'logfO2' column found. Attempting to find a column for aqueous O2 to estimate logfO2 at sample temperature and pressure...
2026-01-05T01:34:12.1991963Z Using wrm to speciate Bison Pool
2026-01-05T01:34:12.1992338Z Using wrm to speciate Spray Geyser Source
2026-01-05T01:34:12.1993146Z Warning: non-numeric aqueous O2 value in sample Crater Hills Geyser. Resorting to using Log fO2 (log bars) with a value of -6
2026-01-05T01:34:12.1993953Z Using wrm to speciate Crater Hills Geyser
2026-01-05T01:34:12.1994346Z Using wrm to speciate Ambergris
2026-01-05T01:34:12.1994693Z Using wrm to speciate MLS Source
2026-01-05T01:34:12.1995046Z Using wrm to speciate Gas Crack
2026-01-05T01:34:12.1995378Z Using wrm to speciate Snail
2026-01-05T01:34:12.1995687Z Finished!
2026-01-05T01:34:12.1995943Z [OK] Speciation completed
2026-01-05T01:34:12.1996460Z [OK] aq_distribution is a DataFrame with 81 rows
2026-01-05T01:34:12.1996751Z 
2026-01-05T01:34:12.1996895Z ============================================================
2026-01-05T01:34:12.1997301Z Test 6: Testing water-rock reaction
2026-01-05T01:34:12.1997687Z ============================================================
2026-01-05T01:34:12.1998564Z Running speciation on /opt/hostedtoolcache/Python/3.13.11/x64/lib/python3.13/site-packages/aqequil/test_data/input_example_wrm.csv...
2026-01-05T01:34:12.1999485Z [INFO] Working directory: /tmp/tmpstwx53wg
2026-01-05T01:34:12.2000013Z [OK] Copied wrm_data_latest.csv to bundled databases (replaced existing)
2026-01-05T01:34:12.2000646Z [OK] Copied elements.csv to bundled databases (replaced existing)
2026-01-05T01:34:12.2001404Z [OK] Copied solid_solutions.csv to bundled databases (replaced existing)
2026-01-05T01:34:12.2002108Z [OK] Copied wrm_data_logk.csv to bundled databases (replaced existing)
2026-01-05T01:34:12.2002751Z [OK] Copied wrm_data_logk_s.csv to bundled databases (replaced existing)
2026-01-05T01:34:12.2003766Z The input file column 'logfO2' will be used to set sample redox state. If a another column is desired, set it manually using the redox_flag parameter.
2026-01-05T01:34:12.2004751Z Getting wrm_data_latest.csv ready. This will take a moment...
2026-01-05T01:34:12.2005518Z No 'charge_balance_on' column found in input file. Defaulting to no charge balancing for all samples.
2026-01-05T01:34:12.2006738Z Warning: a column for Pressure was not found in the sample input file. Defaulting to water saturation pressure...
2026-01-05T01:34:12.2007911Z Warning: no 'logfO2' column found. Attempting to find a column for aqueous O2 to estimate logfO2 at sample temperature and pressure...
2026-01-05T01:34:12.2008828Z Using wrm_data_latest.csv to speciate Bison Pool
2026-01-05T01:34:12.2009533Z Using wrm_data_latest.csv to speciate Spray Geyser Source
2026-01-05T01:34:12.2010395Z Warning: non-numeric aqueous O2 value in sample Crater Hills Geyser. Resorting to using Log fO2 (log bars) with a value of -6
2026-01-05T01:34:12.2011265Z Using wrm_data_latest.csv to speciate Crater Hills Geyser
2026-01-05T01:34:12.2012087Z Using wrm_data_latest.csv to speciate Ambergris
2026-01-05T01:34:12.2012588Z Using wrm_data_latest.csv to speciate MLS Source
2026-01-05T01:34:12.2013030Z Using wrm_data_latest.csv to speciate Gas Crack
2026-01-05T01:34:12.2013484Z Using wrm_data_latest.csv to speciate Snail
2026-01-05T01:34:12.2013880Z Finished!
2026-01-05T01:34:12.2014153Z [OK] Initial speciation completed
2026-01-05T01:34:12.2014509Z [OK] Reaction prepared
2026-01-05T01:34:12.2014847Z Running water-rock reaction...
2026-01-05T01:34:12.2015221Z Using wrm_data_latest.csv to react Bison.Pool
2026-01-05T01:34:12.2015522Z 
2026-01-05T01:34:12.2015769Z The sample 'Bison Pool' experienced errors during the reaction:
2026-01-05T01:34:12.2016616Z  * Error - (EQ6/intmtb) A mass balance is defined on the input
2026-01-05T01:34:12.2017209Z        file for NH4+ (Aqueous solution), but this species isn't in the
2026-01-05T01:34:12.2017849Z        currently active basis set. Either it isn't on the current data file
2026-01-05T01:34:12.2018483Z        or it has been suppressed as by an nxmod or iopt(15) option.
2026-01-05T01:34:12.2018870Z 
2026-01-05T01:34:12.2019384Z Mass transfer results for sample 'Bison Pool' could not be saved because the calculation did not finish due to error(s).
2026-01-05T01:34:12.2020047Z 
2026-01-05T01:34:12.2020246Z Using wrm_data_latest.csv to react Spray.Geyser.Source
2026-01-05T01:34:12.2020581Z 
2026-01-05T01:34:12.2020853Z The sample 'Spray Geyser Source' experienced errors during the reaction:
2026-01-05T01:34:12.2021460Z  * Error - (EQ6/intrct) The reactant antigorite isn't among
2026-01-05T01:34:12.2021918Z        the loaded minerals.
2026-01-05T01:34:12.2022131Z 
2026-01-05T01:34:12.2022695Z Mass transfer results for sample 'Spray Geyser Source' could not be saved because the calculation did not finish due to error(s).
2026-01-05T01:34:12.2023387Z 
2026-01-05T01:34:12.2023586Z Using wrm_data_latest.csv to react Crater.Hills.Geyser
2026-01-05T01:34:12.2024062Z Using wrm_data_latest.csv to react Ambergris
2026-01-05T01:34:12.2024497Z Using wrm_data_latest.csv to react MLS.Source
2026-01-05T01:34:12.2024919Z Using wrm_data_latest.csv to react Gas.Crack
2026-01-05T01:34:12.2025188Z 
2026-01-05T01:34:12.2025406Z The sample 'Gas Crack' experienced errors during the reaction:
2026-01-05T01:34:12.2026200Z  * Error - (EQ6/path) The equilibrium calculation failed at the initial value
2026-01-05T01:34:12.2026756Z        of reaction progress.
2026-01-05T01:34:12.2026963Z 
2026-01-05T01:34:12.2027459Z Mass transfer results for sample 'Gas Crack' could not be saved because the calculation did not finish due to error(s).
2026-01-05T01:34:12.2028088Z 
2026-01-05T01:34:12.2028240Z Using wrm_data_latest.csv to react Snail
2026-01-05T01:34:12.2028506Z 
2026-01-05T01:34:12.2028714Z The sample 'Snail' experienced errors during the reaction:
2026-01-05T01:34:12.2029319Z  * Error - (EQ6/path) The equilibrium calculation failed at the initial value
2026-01-05T01:34:12.2029855Z        of reaction progress.
2026-01-05T01:34:12.2030070Z 
2026-01-05T01:34:12.2030563Z Mass transfer results for sample 'Snail' could not be saved because the calculation did not finish due to error(s).
2026-01-05T01:34:12.2031225Z 
2026-01-05T01:34:12.2031343Z [OK] Reaction completed
2026-01-05T01:34:12.2031688Z [OK] misc_params is a DataFrame with 12 rows
2026-01-05T01:34:12.2031967Z 
2026-01-05T01:34:12.2032112Z ============================================================
2026-01-05T01:34:12.2032500Z TEST SUMMARY
2026-01-05T01:34:12.2032792Z ============================================================
2026-01-05T01:34:12.2033178Z [PASS] Bundled Executables
2026-01-05T01:34:12.2033498Z [PASS] Import and Basic Usage
2026-01-05T01:34:12.2034306Z [PASS] Download Latest data0.wrm
2026-01-05T01:34:12.2034671Z [PASS] EQPT Data0 to Data1 Conversion
2026-01-05T01:34:12.2035061Z [PASS] Simple Speciation (wrm database)
2026-01-05T01:34:12.2035445Z [PASS] Water-Rock Reaction
2026-01-05T01:34:12.2035782Z ============================================================
2026-01-05T01:34:12.2036248Z 
2026-01-05T01:34:12.2036559Z [PASS] All tests passed!
2026-01-05T01:34:12.4888499Z Post job cleanup.
2026-01-05T01:34:12.6692874Z Post job cleanup.
2026-01-05T01:34:12.7684048Z [command]/usr/bin/git version
2026-01-05T01:34:12.7723290Z git version 2.52.0
2026-01-05T01:34:12.7768121Z Temporarily overriding HOME='/home/runner/work/_temp/1a5c19f8-68d8-4454-b46e-95d6ff8a7f0c' before making global git config changes
2026-01-05T01:34:12.7769411Z Adding repository directory to the temporary git global config as a safe directory
2026-01-05T01:34:12.7773966Z [command]/usr/bin/git config --global --add safe.directory /home/runner/work/aqequil/aqequil
2026-01-05T01:34:12.7820124Z [command]/usr/bin/git config --local --name-only --get-regexp core\.sshCommand
2026-01-05T01:34:12.7855823Z [command]/usr/bin/git submodule foreach --recursive sh -c "git config --local --name-only --get-regexp 'core\.sshCommand' && git config --local --unset-all 'core.sshCommand' || :"
2026-01-05T01:34:12.8131545Z [command]/usr/bin/git config --local --name-only --get-regexp http\.https\:\/\/github\.com\/\.extraheader
2026-01-05T01:34:12.8159962Z http.https://github.com/.extraheader
2026-01-05T01:34:12.8176537Z [command]/usr/bin/git config --local --unset-all http.https://github.com/.extraheader
2026-01-05T01:34:12.8215169Z [command]/usr/bin/git submodule foreach --recursive sh -c "git config --local --name-only --get-regexp 'http\.https\:\/\/github\.com\/\.extraheader' && git config --local --unset-all 'http.https://github.com/.extraheader' || :"
2026-01-05T01:34:12.8487299Z [command]/usr/bin/git config --local --name-only --get-regexp ^includeIf\.gitdir:
2026-01-05T01:34:12.8527730Z [command]/usr/bin/git submodule foreach --recursive git config --local --show-origin --name-only --get-regexp remote.origin.url
2026-01-05T01:34:12.8912614Z Cleaning up orphan processes
