﻿2026-01-05T01:33:07.9480360Z Current runner version: '2.330.0'
2026-01-05T01:33:07.9502970Z ##[group]Runner Image Provisioner
2026-01-05T01:33:07.9503729Z Hosted Compute Agent
2026-01-05T01:33:07.9504393Z Version: 20251211.462
2026-01-05T01:33:07.9504974Z Commit: 6cbad8c2bb55d58165063d031ccabf57e2d2db61
2026-01-05T01:33:07.9505671Z Build Date: 2025-12-11T16:28:49Z
2026-01-05T01:33:07.9506425Z Worker ID: {82ba825c-ee9b-4ce6-b4d6-0707e0cfa9ff}
2026-01-05T01:33:07.9507172Z ##[endgroup]
2026-01-05T01:33:07.9507707Z ##[group]Operating System
2026-01-05T01:33:07.9508602Z Ubuntu
2026-01-05T01:33:07.9509085Z 24.04.3
2026-01-05T01:33:07.9509742Z LTS
2026-01-05T01:33:07.9510313Z ##[endgroup]
2026-01-05T01:33:07.9510856Z ##[group]Runner Image
2026-01-05T01:33:07.9511432Z Image: ubuntu-24.04
2026-01-05T01:33:07.9511988Z Version: 20251215.174.1
2026-01-05T01:33:07.9513058Z Included Software: https://github.com/actions/runner-images/blob/ubuntu24/20251215.174/images/ubuntu/Ubuntu2404-Readme.md
2026-01-05T01:33:07.9514647Z Image Release: https://github.com/actions/runner-images/releases/tag/ubuntu24%2F20251215.174
2026-01-05T01:33:07.9515670Z ##[endgroup]
2026-01-05T01:33:07.9518335Z ##[group]GITHUB_TOKEN Permissions
2026-01-05T01:33:07.9520766Z Actions: write
2026-01-05T01:33:07.9521372Z ArtifactMetadata: write
2026-01-05T01:33:07.9521958Z Attestations: write
2026-01-05T01:33:07.9522500Z Checks: write
2026-01-05T01:33:07.9522962Z Contents: write
2026-01-05T01:33:07.9523507Z Deployments: write
2026-01-05T01:33:07.9524105Z Discussions: write
2026-01-05T01:33:07.9524616Z Issues: write
2026-01-05T01:33:07.9525177Z Metadata: read
2026-01-05T01:33:07.9525740Z Models: read
2026-01-05T01:33:07.9526271Z Packages: write
2026-01-05T01:33:07.9526759Z Pages: write
2026-01-05T01:33:07.9527393Z PullRequests: write
2026-01-05T01:33:07.9528055Z RepositoryProjects: write
2026-01-05T01:33:07.9528622Z SecurityEvents: write
2026-01-05T01:33:07.9529265Z Statuses: write
2026-01-05T01:33:07.9530024Z ##[endgroup]
2026-01-05T01:33:07.9532359Z Secret source: Actions
2026-01-05T01:33:07.9533444Z Prepare workflow directory
2026-01-05T01:33:07.9846384Z Prepare all required actions
2026-01-05T01:33:07.9884003Z Getting action download info
2026-01-05T01:33:08.3180301Z Download action repository 'actions/checkout@v4' (SHA:34e114876b0b11c390a56381ad16ebd13914f8d5)
2026-01-05T01:33:08.4057001Z Download action repository 'actions/setup-python@v5' (SHA:a26af69be951a213d495a4c3e4e4022e16d87065)
2026-01-05T01:33:08.4902112Z Download action repository 'actions/download-artifact@v4' (SHA:d3f86a106a0bac45b974a628896c90dbdf5c8093)
2026-01-05T01:33:09.2628673Z Complete job name: Test wheels on ubuntu-latest with Python 3.11
2026-01-05T01:33:09.3374589Z ##[group]Run actions/checkout@v4
2026-01-05T01:33:09.3375878Z with:
2026-01-05T01:33:09.3376623Z   repository: worm-portal/aqequil
2026-01-05T01:33:09.3377831Z   token: ***
2026-01-05T01:33:09.3378551Z   ssh-strict: true
2026-01-05T01:33:09.3379294Z   ssh-user: git
2026-01-05T01:33:09.3380207Z   persist-credentials: true
2026-01-05T01:33:09.3381048Z   clean: true
2026-01-05T01:33:09.3381831Z   sparse-checkout-cone-mode: true
2026-01-05T01:33:09.3382749Z   fetch-depth: 1
2026-01-05T01:33:09.3383476Z   fetch-tags: false
2026-01-05T01:33:09.3384230Z   show-progress: true
2026-01-05T01:33:09.3384988Z   lfs: false
2026-01-05T01:33:09.3385690Z   submodules: false
2026-01-05T01:33:09.3386520Z   set-safe-directory: true
2026-01-05T01:33:09.3387611Z ##[endgroup]
2026-01-05T01:33:09.4467176Z Syncing repository: worm-portal/aqequil
2026-01-05T01:33:09.4469811Z ##[group]Getting Git version info
2026-01-05T01:33:09.4471057Z Working directory is '/home/runner/work/aqequil/aqequil'
2026-01-05T01:33:09.4472884Z [command]/usr/bin/git version
2026-01-05T01:33:09.4535971Z git version 2.52.0
2026-01-05T01:33:09.4562946Z ##[endgroup]
2026-01-05T01:33:09.4579355Z Temporarily overriding HOME='/home/runner/work/_temp/f5965ce5-778c-462b-9003-11089ecd936c' before making global git config changes
2026-01-05T01:33:09.4584377Z Adding repository directory to the temporary git global config as a safe directory
2026-01-05T01:33:09.4593791Z [command]/usr/bin/git config --global --add safe.directory /home/runner/work/aqequil/aqequil
2026-01-05T01:33:09.4632915Z Deleting the contents of '/home/runner/work/aqequil/aqequil'
2026-01-05T01:33:09.4636709Z ##[group]Initializing the repository
2026-01-05T01:33:09.4641934Z [command]/usr/bin/git init /home/runner/work/aqequil/aqequil
2026-01-05T01:33:09.4745295Z hint: Using 'master' as the name for the initial branch. This default branch name
2026-01-05T01:33:09.4747812Z hint: will change to "main" in Git 3.0. To configure the initial branch name
2026-01-05T01:33:09.4750441Z hint: to use in all of your new repositories, which will suppress this warning,
2026-01-05T01:33:09.4752871Z hint: call:
2026-01-05T01:33:09.4754050Z hint:
2026-01-05T01:33:09.4755585Z hint: 	git config --global init.defaultBranch <name>
2026-01-05T01:33:09.4757473Z hint:
2026-01-05T01:33:09.4759216Z hint: Names commonly chosen instead of 'master' are 'main', 'trunk' and
2026-01-05T01:33:09.4762511Z hint: 'development'. The just-created branch can be renamed via this command:
2026-01-05T01:33:09.4764888Z hint:
2026-01-05T01:33:09.4766016Z hint: 	git branch -m <name>
2026-01-05T01:33:09.4767328Z hint:
2026-01-05T01:33:09.4768846Z hint: Disable this message with "git config set advice.defaultBranchName false"
2026-01-05T01:33:09.4771025Z Initialized empty Git repository in /home/runner/work/aqequil/aqequil/.git/
2026-01-05T01:33:09.4774661Z [command]/usr/bin/git remote add origin https://github.com/worm-portal/aqequil
2026-01-05T01:33:09.4798496Z ##[endgroup]
2026-01-05T01:33:09.4800979Z ##[group]Disabling automatic garbage collection
2026-01-05T01:33:09.4803107Z [command]/usr/bin/git config --local gc.auto 0
2026-01-05T01:33:09.4833000Z ##[endgroup]
2026-01-05T01:33:09.4835130Z ##[group]Setting up auth
2026-01-05T01:33:09.4840394Z [command]/usr/bin/git config --local --name-only --get-regexp core\.sshCommand
2026-01-05T01:33:09.4872690Z [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' || :"
2026-01-05T01:33:09.5196033Z [command]/usr/bin/git config --local --name-only --get-regexp http\.https\:\/\/github\.com\/\.extraheader
2026-01-05T01:33:09.5224510Z [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' || :"
2026-01-05T01:33:09.5441728Z [command]/usr/bin/git config --local --name-only --get-regexp ^includeIf\.gitdir:
2026-01-05T01:33:09.5473916Z [command]/usr/bin/git submodule foreach --recursive git config --local --show-origin --name-only --get-regexp remote.origin.url
2026-01-05T01:33:09.5701676Z [command]/usr/bin/git config --local http.https://github.com/.extraheader AUTHORIZATION: basic ***
2026-01-05T01:33:09.5734935Z ##[endgroup]
2026-01-05T01:33:09.5737178Z ##[group]Fetching the repository
2026-01-05T01:33:09.5745886Z [command]/usr/bin/git -c protocol.version=2 fetch --no-tags --prune --no-recurse-submodules --depth=1 origin +0fba8641708a9a29f5cf75d5e1aa5af56402a902:refs/tags/v1.0.1
2026-01-05T01:33:10.0568926Z From https://github.com/worm-portal/aqequil
2026-01-05T01:33:10.0570617Z  * [new ref]         0fba8641708a9a29f5cf75d5e1aa5af56402a902 -> v1.0.1
2026-01-05T01:33:10.0598497Z ##[endgroup]
2026-01-05T01:33:10.0600094Z ##[group]Determining the checkout info
2026-01-05T01:33:10.0601693Z ##[endgroup]
2026-01-05T01:33:10.0605905Z [command]/usr/bin/git sparse-checkout disable
2026-01-05T01:33:10.0646927Z [command]/usr/bin/git config --local --unset-all extensions.worktreeConfig
2026-01-05T01:33:10.0673543Z ##[group]Checking out the ref
2026-01-05T01:33:10.0677220Z [command]/usr/bin/git checkout --progress --force refs/tags/v1.0.1
2026-01-05T01:33:10.1602496Z Note: switching to 'refs/tags/v1.0.1'.
2026-01-05T01:33:10.1603074Z 
2026-01-05T01:33:10.1603560Z You are in 'detached HEAD' state. You can look around, make experimental
2026-01-05T01:33:10.1604916Z changes and commit them, and you can discard any commits you make in this
2026-01-05T01:33:10.1605935Z state without impacting any branches by switching back to a branch.
2026-01-05T01:33:10.1606567Z 
2026-01-05T01:33:10.1607016Z If you want to create a new branch to retain commits you create, you may
2026-01-05T01:33:10.1608012Z do so (now or later) by using -c with the switch command. Example:
2026-01-05T01:33:10.1608600Z 
2026-01-05T01:33:10.1608880Z   git switch -c <new-branch-name>
2026-01-05T01:33:10.1609300Z 
2026-01-05T01:33:10.1609761Z Or undo this operation with:
2026-01-05T01:33:10.1610174Z 
2026-01-05T01:33:10.1610418Z   git switch -
2026-01-05T01:33:10.1610742Z 
2026-01-05T01:33:10.1611040Z Turn off this advice by setting config variable advice.detachedHead to false
2026-01-05T01:33:10.1611468Z 
2026-01-05T01:33:10.1611786Z HEAD is now at 0fba864 Add automatic versioning from git tags using setuptools_scm
2026-01-05T01:33:10.1616218Z ##[endgroup]
2026-01-05T01:33:10.1653040Z [command]/usr/bin/git log -1 --format=%H
2026-01-05T01:33:10.1674669Z 0fba8641708a9a29f5cf75d5e1aa5af56402a902
2026-01-05T01:33:10.1910319Z ##[group]Run actions/setup-python@v5
2026-01-05T01:33:10.1910779Z with:
2026-01-05T01:33:10.1911101Z   python-version: 3.11
2026-01-05T01:33:10.1911447Z   check-latest: false
2026-01-05T01:33:10.1911920Z   token: ***
2026-01-05T01:33:10.1912241Z   update-environment: true
2026-01-05T01:33:10.1912602Z   allow-prereleases: false
2026-01-05T01:33:10.1912954Z   freethreaded: false
2026-01-05T01:33:10.1913266Z ##[endgroup]
2026-01-05T01:33:10.3628917Z ##[group]Installed versions
2026-01-05T01:33:10.3729797Z Successfully set up CPython (3.11.14)
2026-01-05T01:33:10.3731299Z ##[endgroup]
2026-01-05T01:33:10.3868141Z ##[group]Run actions/download-artifact@v4
2026-01-05T01:33:10.3868585Z with:
2026-01-05T01:33:10.3868885Z   name: wheels-ubuntu-latest
2026-01-05T01:33:10.3869246Z   path: wheelhouse
2026-01-05T01:33:10.3869738Z   merge-multiple: false
2026-01-05T01:33:10.3870114Z   repository: worm-portal/aqequil
2026-01-05T01:33:10.3870482Z   run-id: 20702070857
2026-01-05T01:33:10.3870781Z env:
2026-01-05T01:33:10.3871154Z   pythonLocation: /opt/hostedtoolcache/Python/3.11.14/x64
2026-01-05T01:33:10.3871761Z   PKG_CONFIG_PATH: /opt/hostedtoolcache/Python/3.11.14/x64/lib/pkgconfig
2026-01-05T01:33:10.3872347Z   Python_ROOT_DIR: /opt/hostedtoolcache/Python/3.11.14/x64
2026-01-05T01:33:10.3872862Z   Python2_ROOT_DIR: /opt/hostedtoolcache/Python/3.11.14/x64
2026-01-05T01:33:10.3873382Z   Python3_ROOT_DIR: /opt/hostedtoolcache/Python/3.11.14/x64
2026-01-05T01:33:10.3873908Z   LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.11.14/x64/lib
2026-01-05T01:33:10.3874344Z ##[endgroup]
2026-01-05T01:33:10.5797935Z Downloading single artifact
2026-01-05T01:33:10.7136260Z Preparing to download the following artifacts:
2026-01-05T01:33:10.7137737Z - wheels-ubuntu-latest (ID: 5019911133, Size: 24825482, Expected Digest: sha256:a6d43ff313b13b3a568b82ecd8c330433356ae553a4f11dccf013c81efd55f84)
2026-01-05T01:33:10.8011831Z 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
2026-01-05T01:33:10.8014022Z Starting download of artifact to: /home/runner/work/aqequil/aqequil/wheelhouse
2026-01-05T01:33:10.9406517Z (node:2122) [DEP0005] DeprecationWarning: Buffer() is deprecated due to security and usability issues. Please use the Buffer.alloc(), Buffer.allocUnsafe(), or Buffer.from() methods instead.
2026-01-05T01:33:10.9408463Z (Use `node --trace-deprecation ...` to show where the warning was created)
2026-01-05T01:33:11.5358548Z SHA256 digest of downloaded artifact is a6d43ff313b13b3a568b82ecd8c330433356ae553a4f11dccf013c81efd55f84
2026-01-05T01:33:11.5360032Z Artifact download completed successfully.
2026-01-05T01:33:11.5360611Z Total of 1 artifact(s) downloaded
2026-01-05T01:33:11.5368835Z Download artifact has finished successfully
2026-01-05T01:33:11.5522454Z ##[group]Run PYVER=$(echo "3.11" | tr -d '.')
2026-01-05T01:33:11.5522868Z [36;1mPYVER=$(echo "3.11" | tr -d '.')[0m
2026-01-05T01:33:11.5523248Z [36;1mpython -m pip install wheelhouse/aqequil-*-cp${PYVER}-*.whl[0m
2026-01-05T01:33:11.5570782Z shell: /usr/bin/bash --noprofile --norc -e -o pipefail {0}
2026-01-05T01:33:11.5571142Z env:
2026-01-05T01:33:11.5571400Z   pythonLocation: /opt/hostedtoolcache/Python/3.11.14/x64
2026-01-05T01:33:11.5571836Z   PKG_CONFIG_PATH: /opt/hostedtoolcache/Python/3.11.14/x64/lib/pkgconfig
2026-01-05T01:33:11.5572263Z   Python_ROOT_DIR: /opt/hostedtoolcache/Python/3.11.14/x64
2026-01-05T01:33:11.5572653Z   Python2_ROOT_DIR: /opt/hostedtoolcache/Python/3.11.14/x64
2026-01-05T01:33:11.5573038Z   Python3_ROOT_DIR: /opt/hostedtoolcache/Python/3.11.14/x64
2026-01-05T01:33:11.5573443Z   LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.11.14/x64/lib
2026-01-05T01:33:11.5573786Z ##[endgroup]
2026-01-05T01:33:12.2104482Z Processing ./wheelhouse/aqequil-1.0.2.dev0+g0fba86417.d20260105-cp311-cp311-manylinux_2_28_x86_64.whl
2026-01-05T01:33:12.4354874Z Collecting pandas (from aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:12.5256262Z   Downloading pandas-2.3.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (91 kB)
2026-01-05T01:33:12.7667526Z Collecting numpy (from aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:12.7820273Z   Downloading numpy-2.4.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (6.6 kB)
2026-01-05T01:33:12.9060303Z Collecting matplotlib (from aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:12.9211834Z   Downloading matplotlib-3.10.8-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (52 kB)
2026-01-05T01:33:12.9685672Z Collecting plotly (from aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:12.9831296Z   Downloading plotly-6.5.0-py3-none-any.whl.metadata (8.5 kB)
2026-01-05T01:33:13.0427651Z Collecting ipython (from aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:13.0587631Z   Downloading ipython-9.8.0-py3-none-any.whl.metadata (4.5 kB)
2026-01-05T01:33:13.0841732Z Collecting chemparse (from aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:13.0985231Z   Downloading chemparse-0.3.2-py3-none-any.whl.metadata (1.7 kB)
2026-01-05T01:33:13.1126610Z Collecting dill (from aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:13.1268383Z   Downloading dill-0.4.0-py3-none-any.whl.metadata (10 kB)
2026-01-05T01:33:13.1420834Z Collecting periodictable (from aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:13.1564376Z   Downloading periodictable-2.0.2-py3-none-any.whl.metadata (5.4 kB)
2026-01-05T01:33:13.1819071Z Collecting natsort (from aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:13.1964717Z   Downloading natsort-8.4.0-py3-none-any.whl.metadata (21 kB)
2026-01-05T01:33:13.2106346Z Collecting roman (from aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:13.2254198Z   Downloading roman-5.2-py3-none-any.whl.metadata (4.3 kB)
2026-01-05T01:33:13.2577128Z Collecting ipywidgets (from aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:13.2724395Z   Downloading ipywidgets-8.1.8-py3-none-any.whl.metadata (2.4 kB)
2026-01-05T01:33:13.2900735Z Collecting wormutils (from aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:13.3049870Z   Downloading wormutils-0.2.0-py3-none-any.whl.metadata (723 bytes)
2026-01-05T01:33:13.3314751Z Collecting pychnosz (from aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:13.4714676Z   Downloading pychnosz-1.1.12-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (8.2 kB)
2026-01-05T01:33:13.4893760Z Collecting decorator>=4.3.2 (from ipython->aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:13.5041877Z   Downloading decorator-5.2.1-py3-none-any.whl.metadata (3.9 kB)
2026-01-05T01:33:13.5140769Z Collecting ipython-pygments-lexers>=1.0.0 (from ipython->aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:13.5290190Z   Downloading ipython_pygments_lexers-1.1.1-py3-none-any.whl.metadata (1.1 kB)
2026-01-05T01:33:13.5418082Z Collecting jedi>=0.18.1 (from ipython->aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:13.5566305Z   Downloading jedi-0.19.2-py2.py3-none-any.whl.metadata (22 kB)
2026-01-05T01:33:13.5721428Z Collecting matplotlib-inline>=0.1.5 (from ipython->aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:13.5865014Z   Downloading matplotlib_inline-0.2.1-py3-none-any.whl.metadata (2.3 kB)
2026-01-05T01:33:13.5980832Z Collecting pexpect>4.3 (from ipython->aqequil==1.0.2.dev0+g0fba86417.d20260105)
2026-01-05T01:33:13.6125178Z   Downloading pexpect-4.9.0-py2.py3-none-any.whl.metadata (2.5 kB)
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2026-01-05T01:33:18.3798748Z Downloading charset_normalizer-3.4.4-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (151 kB)
2026-01-05T01:33:18.3969892Z Downloading idna-3.11-py3-none-any.whl (71 kB)
2026-01-05T01:33:18.4140175Z Downloading urllib3-2.6.2-py3-none-any.whl (131 kB)
2026-01-05T01:33:18.4310806Z Downloading certifi-2026.1.4-py3-none-any.whl (152 kB)
2026-01-05T01:33:18.7223749Z Installing collected packages: pytz, pure-eval, ptyprocess, widgetsnbextension, wcwidth, urllib3, tzdata, typing_extensions, 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
2026-01-05T01:33:36.1158827Z 
2026-01-05T01:33:36.1191175Z 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 typing_extensions-4.15.0 tzdata-2025.3 urllib3-2.6.2 wcwidth-0.2.14 widgetsnbextension-4.0.15 wormutils-0.2.0
2026-01-05T01:33:36.4230750Z ##[group]Run cp "$GITHUB_WORKSPACE/test_integration.py" "$RUNNER_TEMP/"
2026-01-05T01:33:36.4231247Z [36;1mcp "$GITHUB_WORKSPACE/test_integration.py" "$RUNNER_TEMP/"[0m
2026-01-05T01:33:36.4231575Z [36;1mcd "$RUNNER_TEMP"[0m
2026-01-05T01:33:36.4231809Z [36;1mpython test_integration.py[0m
2026-01-05T01:33:36.4265081Z shell: /usr/bin/bash --noprofile --norc -e -o pipefail {0}
2026-01-05T01:33:36.4265387Z env:
2026-01-05T01:33:36.4265626Z   pythonLocation: /opt/hostedtoolcache/Python/3.11.14/x64
2026-01-05T01:33:36.4266027Z   PKG_CONFIG_PATH: /opt/hostedtoolcache/Python/3.11.14/x64/lib/pkgconfig
2026-01-05T01:33:36.4266421Z   Python_ROOT_DIR: /opt/hostedtoolcache/Python/3.11.14/x64
2026-01-05T01:33:36.4266774Z   Python2_ROOT_DIR: /opt/hostedtoolcache/Python/3.11.14/x64
2026-01-05T01:33:36.4267131Z   Python3_ROOT_DIR: /opt/hostedtoolcache/Python/3.11.14/x64
2026-01-05T01:33:36.4267485Z   LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.11.14/x64/lib
2026-01-05T01:33:36.4267810Z ##[endgroup]
2026-01-05T01:34:05.0083008Z 
2026-01-05T01:34:05.0083454Z ============================================================
2026-01-05T01:34:05.0083944Z AQEQUIL INTEGRATION TEST SUITE
2026-01-05T01:34:05.0084331Z ============================================================
2026-01-05T01:34:05.0084762Z Python: 3.11.14
2026-01-05T01:34:05.0085041Z Platform: linux
2026-01-05T01:34:05.0085321Z Architecture: x86_64
2026-01-05T01:34:05.0085650Z ============================================================
2026-01-05T01:34:05.0086057Z ============================================================
2026-01-05T01:34:05.0086505Z Test 1: Checking for bundled EQ3/6 executables
2026-01-05T01:34:05.0086971Z ============================================================
2026-01-05T01:34:05.0087850Z [OK] Found bundled executables at: /opt/hostedtoolcache/Python/3.11.14/x64/lib/python3.11/site-packages/aqequil/bin
2026-01-05T01:34:05.0088768Z   [OK] eq3nr (1.04 MB)
2026-01-05T01:34:05.0089087Z   [OK] eq6 (1.76 MB)
2026-01-05T01:34:05.0089446Z   [OK] eqpt (0.62 MB)
2026-01-05T01:34:05.0089854Z 
2026-01-05T01:34:05.0090008Z ============================================================
2026-01-05T01:34:05.0090477Z Test 2: Testing aqequil import and basic usage
2026-01-05T01:34:05.0090778Z ============================================================
2026-01-05T01:34:05.0091069Z [OK] Successfully imported aqequil
2026-01-05T01:34:05.0091617Z [OK] Found test data at: /opt/hostedtoolcache/Python/3.11.14/x64/lib/python3.11/site-packages/aqequil/test_data/input_example_wrm.csv
2026-01-05T01:34:05.0092084Z 
2026-01-05T01:34:05.0092179Z ============================================================
2026-01-05T01:34:05.0092494Z Test 3: Downloading latest data0.wrm from WORM-db
2026-01-05T01:34:05.0092775Z ============================================================
2026-01-05T01:34:05.0093256Z Downloading data0.wrm from https://raw.githubusercontent.com/worm-portal/WORM-db/master/data0.wrm...
2026-01-05T01:34:05.0093730Z [OK] Downloaded data0.wrm (573.8 KB)
2026-01-05T01:34:05.0094013Z [OK] Copied data0.wrm to test_data (replaced existing)
2026-01-05T01:34:05.0094332Z [OK] Copied data0.wrm to databases (replaced existing)
2026-01-05T01:34:05.0094535Z 
2026-01-05T01:34:05.0094634Z ============================================================
2026-01-05T01:34:05.0095167Z Test 4: Testing runeqpt (data0 to data1 conversion)
2026-01-05T01:34:05.0095447Z ============================================================
2026-01-05T01:34:05.0095721Z [INFO] Working directory: /tmp/tmpqep9qbnl
2026-01-05T01:34:05.0095991Z [OK] Copied data0.wrm to working directory
2026-01-05T01:34:05.0096247Z Running EQPT on data0.wrm...
2026-01-05T01:34:05.0096451Z [OK] EQPT completed
2026-01-05T01:34:05.0096643Z [OK] data1.wrm created (0.36 MB)
2026-01-05T01:34:05.0096933Z [OK] Copied data1.wrm to bundled databases (replaced existing)
2026-01-05T01:34:05.0097161Z 
2026-01-05T01:34:05.0097250Z ============================================================
2026-01-05T01:34:05.0097713Z Test 5: Testing simple speciation (wrm database)
2026-01-05T01:34:05.0098001Z ============================================================
2026-01-05T01:34:05.0098558Z Running speciation on /opt/hostedtoolcache/Python/3.11.14/x64/lib/python3.11/site-packages/aqequil/test_data/input_example_wrm.csv...
2026-01-05T01:34:05.0099126Z [INFO] Working directory: /tmp/tmpen18haxf
2026-01-05T01:34:05.0099393Z [OK] Copied data0.wrm to working directory
2026-01-05T01:34:05.0099968Z Running EQPT to create data1.wrm...
2026-01-05T01:34:05.0100216Z [OK] EQPT completed, data1.wrm created
2026-01-05T01:34:05.0100490Z [OK] AqEquil instance created with wrm database
2026-01-05T01:34:05.0101094Z 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.
2026-01-05T01:34:05.0101856Z No 'charge_balance_on' column found in input file. Defaulting to no charge balancing for all samples.
2026-01-05T01:34:05.0102575Z Warning: no 'logfO2' column found. Attempting to find a column for aqueous O2 to estimate logfO2 at sample temperature and pressure...
2026-01-05T01:34:05.0103116Z Using wrm to speciate Bison Pool
2026-01-05T01:34:05.0103365Z Using wrm to speciate Spray Geyser Source
2026-01-05T01:34:05.0103893Z Warning: non-numeric aqueous O2 value in sample Crater Hills Geyser. Resorting to using Log fO2 (log bars) with a value of -6
2026-01-05T01:34:05.0104434Z Using wrm to speciate Crater Hills Geyser
2026-01-05T01:34:05.0104686Z Using wrm to speciate Ambergris
2026-01-05T01:34:05.0104939Z Using wrm to speciate MLS Source
2026-01-05T01:34:05.0105160Z Using wrm to speciate Gas Crack
2026-01-05T01:34:05.0105377Z Using wrm to speciate Snail
2026-01-05T01:34:05.0105583Z Finished!
2026-01-05T01:34:05.0105747Z [OK] Speciation completed
2026-01-05T01:34:05.0105986Z [OK] aq_distribution is a DataFrame with 81 rows
2026-01-05T01:34:05.0106174Z 
2026-01-05T01:34:05.0106271Z ============================================================
2026-01-05T01:34:05.0106531Z Test 6: Testing water-rock reaction
2026-01-05T01:34:05.0106774Z ============================================================
2026-01-05T01:34:05.0107330Z Running speciation on /opt/hostedtoolcache/Python/3.11.14/x64/lib/python3.11/site-packages/aqequil/test_data/input_example_wrm.csv...
2026-01-05T01:34:05.0107898Z [INFO] Working directory: /tmp/tmp23jkg4l1
2026-01-05T01:34:05.0108239Z [OK] Copied wrm_data_latest.csv to bundled databases (replaced existing)
2026-01-05T01:34:05.0108656Z [OK] Copied elements.csv to bundled databases (replaced existing)
2026-01-05T01:34:05.0109141Z [OK] Copied solid_solutions.csv to bundled databases (replaced existing)
2026-01-05T01:34:05.0109745Z [OK] Copied wrm_data_logk.csv to bundled databases (replaced existing)
2026-01-05T01:34:05.0110155Z [OK] Copied wrm_data_logk_s.csv to bundled databases (replaced existing)
2026-01-05T01:34:05.0110821Z 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.
2026-01-05T01:34:05.0111463Z Getting wrm_data_latest.csv ready. This will take a moment...
2026-01-05T01:34:05.0111950Z No 'charge_balance_on' column found in input file. Defaulting to no charge balancing for all samples.
2026-01-05T01:34:05.0112591Z Warning: a column for Pressure was not found in the sample input file. Defaulting to water saturation pressure...
2026-01-05T01:34:05.0113488Z Warning: no 'logfO2' column found. Attempting to find a column for aqueous O2 to estimate logfO2 at sample temperature and pressure...
2026-01-05T01:34:05.0114050Z Using wrm_data_latest.csv to speciate Bison Pool
2026-01-05T01:34:05.0114376Z Using wrm_data_latest.csv to speciate Spray Geyser Source
2026-01-05T01:34:05.0114934Z Warning: non-numeric aqueous O2 value in sample Crater Hills Geyser. Resorting to using Log fO2 (log bars) with a value of -6
2026-01-05T01:34:05.0115502Z Using wrm_data_latest.csv to speciate Crater Hills Geyser
2026-01-05T01:34:05.0116070Z Using wrm_data_latest.csv to speciate Ambergris
2026-01-05T01:34:05.0116647Z Using wrm_data_latest.csv to speciate MLS Source
2026-01-05T01:34:05.0117189Z Using wrm_data_latest.csv to speciate Gas Crack
2026-01-05T01:34:05.0117726Z Using wrm_data_latest.csv to speciate Snail
2026-01-05T01:34:05.0118151Z Finished!
2026-01-05T01:34:05.0118481Z [OK] Initial speciation completed
2026-01-05T01:34:05.0118893Z [OK] Reaction prepared
2026-01-05T01:34:05.0119254Z Running water-rock reaction...
2026-01-05T01:34:05.0119956Z Using wrm_data_latest.csv to react Bison.Pool
2026-01-05T01:34:05.0120167Z 
2026-01-05T01:34:05.0120325Z The sample 'Bison Pool' experienced errors during the reaction:
2026-01-05T01:34:05.0120718Z  * Error - (EQ6/intmtb) A mass balance is defined on the input
2026-01-05T01:34:05.0121102Z        file for NH4+ (Aqueous solution), but this species isn't in the
2026-01-05T01:34:05.0121512Z        currently active basis set. Either it isn't on the current data file
2026-01-05T01:34:05.0121933Z        or it has been suppressed as by an nxmod or iopt(15) option.
2026-01-05T01:34:05.0122161Z 
2026-01-05T01:34:05.0122493Z Mass transfer results for sample 'Bison Pool' could not be saved because the calculation did not finish due to error(s).
2026-01-05T01:34:05.0122906Z 
2026-01-05T01:34:05.0123045Z Using wrm_data_latest.csv to react Spray.Geyser.Source
2026-01-05T01:34:05.0123264Z 
2026-01-05T01:34:05.0123439Z The sample 'Spray Geyser Source' experienced errors during the reaction:
2026-01-05T01:34:05.0123836Z  * Error - (EQ6/intrct) The reactant antigorite isn't among
2026-01-05T01:34:05.0124133Z        the loaded minerals.
2026-01-05T01:34:05.0124261Z 
2026-01-05T01:34:05.0124614Z Mass transfer results for sample 'Spray Geyser Source' could not be saved because the calculation did not finish due to error(s).
2026-01-05T01:34:05.0125064Z 
2026-01-05T01:34:05.0125189Z Using wrm_data_latest.csv to react Crater.Hills.Geyser
2026-01-05T01:34:05.0125498Z Using wrm_data_latest.csv to react Ambergris
2026-01-05T01:34:05.0125779Z Using wrm_data_latest.csv to react MLS.Source
2026-01-05T01:34:05.0126053Z Using wrm_data_latest.csv to react Gas.Crack
2026-01-05T01:34:05.0126231Z 
2026-01-05T01:34:05.0126379Z The sample 'Gas Crack' experienced errors during the reaction:
2026-01-05T01:34:05.0126797Z  * Error - (EQ6/path) The equilibrium calculation failed at the initial value
2026-01-05T01:34:05.0127160Z        of reaction progress.
2026-01-05T01:34:05.0127305Z 
2026-01-05T01:34:05.0127628Z Mass transfer results for sample 'Gas Crack' could not be saved because the calculation did not finish due to error(s).
2026-01-05T01:34:05.0128045Z 
2026-01-05T01:34:05.0128136Z Using wrm_data_latest.csv to react Snail
2026-01-05T01:34:05.0128309Z 
2026-01-05T01:34:05.0128452Z The sample 'Snail' experienced errors during the reaction:
2026-01-05T01:34:05.0128855Z  * Error - (EQ6/path) The equilibrium calculation failed at the initial value
2026-01-05T01:34:05.0129201Z        of reaction progress.
2026-01-05T01:34:05.0129345Z 
2026-01-05T01:34:05.0129785Z Mass transfer results for sample 'Snail' could not be saved because the calculation did not finish due to error(s).
2026-01-05T01:34:05.0130193Z 
2026-01-05T01:34:05.0130274Z [OK] Reaction completed
2026-01-05T01:34:05.0130494Z [OK] misc_params is a DataFrame with 12 rows
2026-01-05T01:34:05.0130684Z 
2026-01-05T01:34:05.0131268Z ============================================================
2026-01-05T01:34:05.0131553Z TEST SUMMARY
2026-01-05T01:34:05.0131756Z ============================================================
2026-01-05T01:34:05.0132026Z [PASS] Bundled Executables
2026-01-05T01:34:05.0132254Z [PASS] Import and Basic Usage
2026-01-05T01:34:05.0132485Z [PASS] Download Latest data0.wrm
2026-01-05T01:34:05.0132721Z [PASS] EQPT Data0 to Data1 Conversion
2026-01-05T01:34:05.0133000Z [PASS] Simple Speciation (wrm database)
2026-01-05T01:34:05.0133256Z [PASS] Water-Rock Reaction
2026-01-05T01:34:05.0133488Z ============================================================
2026-01-05T01:34:05.0133671Z 
2026-01-05T01:34:05.0133875Z [PASS] All tests passed!
2026-01-05T01:34:05.2387639Z Post job cleanup.
2026-01-05T01:34:05.4026258Z Post job cleanup.
2026-01-05T01:34:05.4950984Z [command]/usr/bin/git version
2026-01-05T01:34:05.4986154Z git version 2.52.0
2026-01-05T01:34:05.5029865Z Temporarily overriding HOME='/home/runner/work/_temp/8d2038a3-1b55-482a-a0f0-d55523e11c97' before making global git config changes
2026-01-05T01:34:05.5031237Z Adding repository directory to the temporary git global config as a safe directory
2026-01-05T01:34:05.5036212Z [command]/usr/bin/git config --global --add safe.directory /home/runner/work/aqequil/aqequil
2026-01-05T01:34:05.5076300Z [command]/usr/bin/git config --local --name-only --get-regexp core\.sshCommand
2026-01-05T01:34:05.5108115Z [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' || :"
2026-01-05T01:34:05.5334732Z [command]/usr/bin/git config --local --name-only --get-regexp http\.https\:\/\/github\.com\/\.extraheader
2026-01-05T01:34:05.5355077Z http.https://github.com/.extraheader
2026-01-05T01:34:05.5371124Z [command]/usr/bin/git config --local --unset-all http.https://github.com/.extraheader
2026-01-05T01:34:05.5406275Z [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' || :"
2026-01-05T01:34:05.5654134Z [command]/usr/bin/git config --local --name-only --get-regexp ^includeIf\.gitdir:
2026-01-05T01:34:05.5686761Z [command]/usr/bin/git submodule foreach --recursive git config --local --show-origin --name-only --get-regexp remote.origin.url
2026-01-05T01:34:05.6032867Z Cleaning up orphan processes
