Merge branch 'main' into docs/descriptions-and-errors

.github/workflows/ci.yml

@@ -9,7 +9,7 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: psf/black@stable
   release:
     name: release
@@ -23,7 +23,7 @@ jobs:
         with:
           release-type: python
           package-name: kimmdy
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: tag stable versions
         if: ${{ steps.release.outputs.release_created }}
         run: |
@@ -34,3 +34,35 @@ jobs:
           git push origin :stable || true
           git tag -a stable -m "Last Stable Release"
           git push origin stable
+  prlabel:
+    runs-on: ubuntu-latest
+    outputs:
+      status: ${{ steps.prcheck.conclusion }}
+    steps:
+      - name: Check pr lable
+        id: prcheck
+        uses: jesusvasquez333/verify-pr-label-action@v1.4.0
+        with:
+          github-token: '${{ secrets.GITHUB_TOKEN }}'
+          valid-labels: 'CI:run_test'
+          invalid-labels: ''
+          disable-reviews: true
+  test:
+    runs-on: ubuntu-latest
+    container: riedmiki/gromacs-plumed-python:2021
+    needs: prlabel
+    if: needs.prlabel.outputs.status == 'success'
+    steps:
+      - uses  : actions/checkout@v3
+      - name: run tox
+        run: tox
+      - name: zip coverage report
+        if: ${{ !cancelled() }}
+        run: zip -r htmlcov.zip htmlcov || true
+      - uses: actions/upload-artifact@v3
+        if: ${{ !cancelled() }}
+        with:
+          name: coverage artifact
+          path: htmlcov.zip
+
+

.gitignore

@@ -68,7 +68,9 @@ pip-log.txt
 pip-delete-this-directory.txt
 
 # Unit test / coverage reports
+artifacts
 htmlcov/
+htmlcov*
 .tox/
 .nox/
 .coverage
@@ -109,3 +111,5 @@ package-lock.json
 
 
 /.quarto/
+
+/.luarc.json

README.md

@@ -1,5 +1,7 @@
 # KIMMDY
 
+[![CI](https://github.com/hits-mbm-dev/kimmdy/actions/workflows/ci.yml/badge.svg)](https://github.com/hits-mbm-dev/kimmdy/actions/workflows/ci.yml)
+
 Reactive MD pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamics (KIMMDY)
 
 ## Quick start
@@ -8,8 +10,16 @@ Reactive MD pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamics
 * `cd kimmdy`
 * `python -m venv .venv`
 * `source ./venv/bin/activate`
+* `python -m pip install -e ./`
+* Some rections need a GROMACS version patched with PLUMED, gromacs name should then contain `MODIFIED` or `plumed`
+
+## Development setup
+
 * `python -m pip install -r requirments.txt`
-* Some rections need a GROMACS version patched with PLUMED
+* code style: black
+* docstrings: numpy
+* [Conventional commit](https://www.conventionalcommits.org/en/v1.0.0/) messages when possible for pretty release notes.
+
 
 ## First simulation
 
@@ -19,3 +29,14 @@ Reactive MD pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamics
 * check output: `kimmdy.log`, `test_out_00X/`
 
 
+## Local testing
+
+For developoment, we provide a docker image containing gromacs and multiple python versions to test against.  
+To run the test locally, you must:
+- install docker
+- install [act](https://github.com/nektos/act), easiest option is with github cli
+    - install github cli (`gh`)
+    - `gh extension install https://github.com/nektos/gh-act`
+- run tests with `gh extension exec act -j test --artifact-server-path ./artifacts`
+    - customize which python versions to test in `tox.ini` 
+    - html coverage report is exported into `artifacts`

example/alanine/amber99sb-star-ildnp.ff

@@ -0,0 +1 @@
+../../tests/test_files/assets/amber99sb-star-ildnp.ff

example/example_dryrun/kimmdy.yml → example/alanine/kimmdy.yml

@@ -1,6 +1,8 @@
-dryrun: true
+# yaml-language-server: $schema=../../../../src/kimmdy/kimmdy-yaml-schema.json
+
+dryrun: false
+name: 'alanine_hat_000'
 iterations: 100
-name: 'hat_tf_000'
 gromacs_alias: 'gmx'
 ff: 'amber99sb-star-ildnp.ff' # optional, dir endinng with .ff by default 
 top: 'Ala_out.top'
@@ -10,12 +12,16 @@ mds:
   equilibrium:
     mdp: 'md.mdp'
   relax:
-    mdp: 'md_slow.mdp'
+    mdp: 'md_parameter_growth.mdp'
 changer:
   coordinates:
-    md: 'relax'      
+    md_parameter_growth: 'relax'      
 reactions:
-  hat_naive: {}
+  hat_naive:
+    frequency_factor: 100000000
+    h_cutoff: 3
+    polling_rate: 1
+
 sequence:
 - equilibrium
 - mult: 2

example/example_ala/md.mdp → example/alanine/md.mdp

@@ -1,15 +1,15 @@
 title                   = OPLS Lysozyme NPT equilibration 
 ; Run parameters
 integrator              = md        ; leap-frog integrator
-nsteps                  = 50000     ; 2 * 100000 = 1000 ps (0.2 ns)
+nsteps                  = 5000      ; 0.002 * 5000 = 10ps 
 dt                      = 0.002     ; 2 fs
 ; Output control
-nstenergy               = 5000      ; save energies every 10.0 ps
-nstlog                  = 5000      ; update log file every 10.0 ps
-nstxout			= 5000
-nstvout			= 5000
-nstfout			= 5000
-nstxout-compressed      = 5000      ; save compressed coordinates every 10.0 ps
+nstenergy               = 100       ; save energies every 200.0 fs
+nstlog                  = 100       ; update log file every 200.0 fs
+nstxout                 = 500
+nstvout                 = 500
+nstfout                 = 500
+nstxout-compressed      = 500       ; save compressed coordinates every 1.0 ps
 compressed-x-grps       = System    ; save the whole system
 ; Bond parameters
 continuation            = yes       ; Restarting after NPT 

example/example_triala/md_slow.mdp → example/alanine/md_parameter_growth.mdp

@@ -1,15 +1,15 @@
 title                   = OPLS Lysozyme NPT equilibration 
 ; Run parameters
 integrator              = md        ; leap-frog integrator
-nsteps                  = 5000    ; 2 * 100000 = 1000 ps (0.2 ns)
-dt                      = 0.0002     ; 0.5 fs
+nsteps                  = 5000      ; 0.002 * 5000 = 10ps 
+dt                      = 0.002     ; 2 fs
 ; Output control
-nstenergy               = 5000      ; save energies every 10.0 ps
-nstlog                  = 5000      ; update log file every 10.0 ps
-nstxout			= 1
-nstvout			= 1
-nstfout			= 1
-nstxout-compressed      = 1      ; save compressed coordinates every 10.0 ps
+nstenergy               = 100       ; save energies every 200.0 fs
+nstlog                  = 100       ; update log file every 200.0 fs
+nstxout                 = 500
+nstvout                 = 500
+nstfout                 = 500
+nstxout-compressed      = 500       ; save compressed coordinates every 1.0 ps
 compressed-x-grps       = System    ; save the whole system
 ; Bond parameters
 continuation            = yes       ; Restarting after NPT 
@@ -44,3 +44,9 @@ pbc                     = xyz       ; 3-D PBC
 DispCorr                = EnerPres  ; account for cut-off vdW scheme
 ; Velocity generation
 gen_vel                 = no        ; Velocity generation is off 
+; free-energy parameters
+free-energy             = yes
+init-lambda             = 0.0
+delta-lambda            = 0.0002		; should be 1/nsteps
+separate-dhdl-file      = yes
+nstdhdl                 = 100