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fb4b088
ADding TODO/Comments for things to refactor/review.
ijpulidos Nov 7, 2024
a6a1705
Removing unneeded todo
ijpulidos Nov 20, 2024
24ccc77
Fix custom exceptions in tests
ijpulidos Nov 20, 2024
086f246
Refined dependencies
ijpulidos Dec 5, 2024
e997aea
Misc utility functions and tests
ijpulidos Jan 21, 2025
8fd3877
Adding miscellaneous utility functions
ijpulidos Jan 30, 2025
ad4ef62
Using new utility funcs from both feflow and openfe (branch)
ijpulidos Jan 30, 2025
7b8ab83
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 30, 2025
08aedfe
Using protein mutation support openfe branch for now
ijpulidos Jan 30, 2025
9ad227a
remove conda-forge openfe dependency for now
ijpulidos Jan 30, 2025
5134755
Adding temporary dependencies
ijpulidos Jan 30, 2025
c35439e
WIP -- fixing tests and TODOs
ijpulidos Feb 20, 2025
1139eb2
Doesn't make sense to detect phase. Better name for unit.
ijpulidos Feb 26, 2025
9b2e508
Add utility function to get residue indices in chain
ijpulidos Mar 25, 2025
5784daa
Using mapped atoms instead of unique, since unique can be empty.
ijpulidos Mar 25, 2025
1669449
Using updated arg name
ijpulidos Mar 25, 2025
e32bb67
Test gly to ala. Useful for removing atoms instead of adding.
ijpulidos Mar 25, 2025
aa3ffc2
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 25, 2025
f10415e
Adding threadpoolctl missing dep
ijpulidos Mar 25, 2025
9a8b99c
Using gufe from git. Temporarily.
ijpulidos Mar 25, 2025
a1106b2
Adding needed dependency for gufe
ijpulidos Apr 1, 2025
34b3a4d
Pinning lower lomap version
ijpulidos Apr 11, 2025
e360385
directly getting solvent component
ijpulidos Apr 24, 2025
330a3c3
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 24, 2025
cbd49f3
Handle topologies with multiple chains by checking all atoms
ijpulidos Jun 10, 2025
afa6b95
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 10, 2025
994c2ca
Adding way to store minmized topology pdb. Minor fixes comments/docs.
ijpulidos Jun 13, 2025
ee875ad
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 13, 2025
484ee95
Get solvent component if exists. None otherwise.
ijpulidos Jun 18, 2025
55ba765
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 18, 2025
257000f
We expect proline error test to fail
ijpulidos Jun 24, 2025
8f71796
Adding setup unit to returned units! woops!
ijpulidos Jul 31, 2025
f4f23f8
Testing for basic mapping consistency
ijpulidos Sep 3, 2025
a40b7dc
Adding basic mapping consistency check when creating protocol dag
ijpulidos Sep 3, 2025
1bcfdd3
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 3, 2025
08fcbd1
Skip failing test due to external tools failing.
ijpulidos Sep 16, 2025
138aa95
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 16, 2025
7db8710
Remove rc CI test
ijpulidos Sep 16, 2025
410f769
xfail message added
ijpulidos Sep 16, 2025
5f1d6a2
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 16, 2025
b911c24
skipping instead of xfailing
ijpulidos Sep 16, 2025
a9f5342
Actually skipping now... sigh
ijpulidos Sep 16, 2025
0bedb93
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 16, 2025
3ed8400
Catching unsupported charge change. Fixing test.
ijpulidos Sep 16, 2025
8e98b7a
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 16, 2025
0697d50
Trying using number of logical cores instead.
ijpulidos Sep 17, 2025
0322437
Vendoring openfe modeller utility
ijpulidos Sep 24, 2025
09bec3f
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 24, 2025
e2a5a92
removing pip deps
ijpulidos Sep 24, 2025
a83fb30
No pydantic 1 in CI.
ijpulidos Sep 24, 2025
f337ef8
We expect openfe >=1.3.0 for omm_compute utils
ijpulidos Sep 24, 2025
03b255a
pymbar 4 BAR changes
ijpulidos Sep 24, 2025
d49925b
we now require pymbar 4
ijpulidos Sep 24, 2025
e3c174b
Fixing codecov repo ref
ijpulidos Sep 24, 2025
d10be95
Using vendore openff model/type from gufe
ijpulidos Sep 24, 2025
644486e
Vendoring get_system_mappings from openfe
ijpulidos Sep 24, 2025
551531d
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 24, 2025
6676349
making pre-commit happy. {} instead of dict()
ijpulidos Sep 24, 2025
b95d0b0
Remving restriction on resids!
ijpulidos Sep 24, 2025
f12c407
Fixing missing pymbar change on boostrapping
ijpulidos Sep 24, 2025
f98a0a5
Serializing HTF right after its creation.
ijpulidos Oct 3, 2025
89c1cfe
Revert "Vendoring get_system_mappings from openfe"
ijpulidos Oct 17, 2025
04c0d1c
We require openfe 1.6.1 (or newer).
ijpulidos Oct 17, 2025
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10 changes: 4 additions & 6 deletions .github/workflows/ci.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -23,12 +23,11 @@ defaults:
jobs:
tests:
runs-on: ${{ matrix.os }}-latest
name: "💻-${{matrix.os }} 🐍-${{ matrix.python-version }} - pydantic ${{matrix.pydantic}}"
name: "💻-${{matrix.os }} 🐍-${{ matrix.python-version }}"
strategy:
fail-fast: false
matrix:
os: ["ubuntu"]
pydantic: ["1", "2"]
python-version:
- "3.10"
- "3.11"
Expand All @@ -53,7 +52,6 @@ jobs:
cache-downloads: true
create-args: >-
python=${{ matrix.python-version }}
pydantic=${{ matrix.pydantic }}
init-shell: bash

- name: "Install"
Expand Down Expand Up @@ -82,12 +80,12 @@ jobs:
# Set the OFE_SLOW_TESTS to True if running a Cron job
OFE_SLOW_TESTS: ${{ fromJSON('{"false":"false","true":"true"}')[github.event_name != 'pull_request'] }}
run: |
pytest -n auto -v --cov=feflow --cov-report=xml --durations=10
pytest -n logical -v --cov=feflow --cov-report=xml --durations=10

- name: codecov
if: ${{ github.repository == 'choderalab/feflow'
if: ${{ github.repository == 'OpenFreeEnergy/feflow'
&& github.event_name == 'pull_request' }}
uses: codecov/codecov-action@v3
uses: codecov/codecov-action@v4
with:
token: ${{ secrets.CODECOV_TOKEN }}
file: coverage.xml
Expand Down
83 changes: 0 additions & 83 deletions .github/workflows/rc-test.yaml

This file was deleted.

10 changes: 5 additions & 5 deletions devtools/conda-envs/test_env.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -4,16 +4,16 @@ channels:
- openeye
dependencies:
# Base depends
- gufe >=0.9.5
- gufe ~=1.6.0
- numpy
- openfe >=0.15 # TODO: Remove once we don't depend on openfe
- openfe ~=1.6.1 # TODO: Remove once we don't depend on openfe
- openff-units
- openmm
- openmmforcefields >=0.14.1 # TODO: remove when upstream deps fix this
- pymbar <4
- pydantic >=1.10.17
- openmmtools >=0.23.0
- pymbar ~=4.0
- pydantic >=1.10.17, <3
- python

# Testing (optional deps)
- espaloma_charge # To us Espaloma FF in tests
- openeye-toolkits
Expand Down
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