Release workflow

.github/workflows/build.yaml

@@ -27,12 +27,3 @@ jobs:
       - name: Build
         run: |
           pixi build
-
-      # Upload
-      - name: Upload
-        if: ${{ github.ref_name == 'dev' && github.repository_owner == 'Auto-Mech'}}
-        run: |
-          pixi run --frozen -e build upload
-        env:
-          ANACONDA_API_KEY: ${{ secrets.ANACONDA_API_KEY }}
-        continue-on-error: true

.github/workflows/release.yaml

@@ -0,0 +1,103 @@
+name: release
+
+on:
+  pull_request_target:
+    types: [closed]
+
+permissions:
+  contents: write
+
+jobs:
+  release:
+    if: >
+      github.event.pull_request.merged == true && (
+        contains(github.event.pull_request.labels.*.name, 'release:patch') ||
+        contains(github.event.pull_request.labels.*.name, 'release:major')
+      )
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: true
+    defaults:
+      run:
+        working-directory: mechdriver
+
+    steps:
+      # 1. Checkout the repositories
+      - name: Checkout merged mechdriver
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.event.pull_request.base.ref }}
+          fetch-depth: 0
+          path: mechdriver
+
+      - name: Checkout autochem
+        uses: actions/checkout@v4
+        with:
+          repository: Auto-Mech/autochem
+          path: autochem
+
+      - name: Checkout autoio
+        uses: actions/checkout@v4
+        with:
+          repository: Auto-Mech/autoio
+          path: autoio
+
+      - name: Checkout autofile
+        uses: actions/checkout@v4
+        with:
+          repository: Auto-Mech/autofile
+          path: autofile
+
+      - name: Checkout mechanalyzer
+        uses: actions/checkout@v4
+        with:
+          repository: Auto-Mech/mechanalyzer
+          path: mechanalyzer
+
+      # 2. Setup environment
+      - name: Set up Pixi
+        uses: prefix-dev/setup-pixi@v0.9.3
+        with:
+          environments: build
+          locked: false
+          manifest-path: mechdriver
+
+      - name: Fetch bot identity
+        id: bot
+        uses: raven-actions/bot-details@v1
+
+      - name: Configure git for committing
+        run: |
+          git config user.name "${{ steps.bot.outputs.name }}"
+          git config user.email "${{ steps.bot.outputs.email }}"
+
+      # 3. Bump version
+      - name: Bump version (patch)
+        if: contains(github.event.pull_request.labels.*.name, 'release:patch')
+        run: pixi run -e build bumpver update --patch
+
+      - name: Bump version (major)
+        if: contains(github.event.pull_request.labels.*.name, 'release:major')
+        run: pixi run -e build bumpver update --major
+
+      - name: Get version
+        id: version
+        run: |
+          echo "tag=$(pixi run current-version)" >> "$GITHUB_OUTPUT"
+
+      # 4. Build and upload conda package
+      - name: Build
+        run: |
+          pixi build
+
+      - name: Upload
+        run: |
+          pixi run -e build upload
+        env:
+          ANACONDA_API_KEY: ${{ secrets.ANACONDA_API_KEY }}
+
+      # 5. Create release
+      - name: Create GitHub Release
+        uses: softprops/action-gh-release@v2
+        with:
+          tag_name: ${{ steps.version.outputs.tag }}

examples/stereo_quick/.gitignore

@@ -0,0 +1,3 @@
+*
+!.gitignore
+!inp/

examples/stereo_quick/inp/.gitignore

@@ -0,0 +1,8 @@
+*
+!.gitignore
+!inp/
+!mechanism.dat
+!models.dat
+!run.dat
+!species.csv
+!theory.dat

examples/stereo_quick/inp/mechanism.dat

@@ -0,0 +1,6 @@
+REACTIONS    CAL/MOL   MOL
+
+C3o2 + OH = C3o2y1r0 + H2O              1.000      0.000      0.000   # pes.subpes.channel  1.1.1
+C3o2 + OH = C3o2y1r1 + H2O              1.000      0.000      0.000   # pes.subpes.channel  1.1.2
+
+END

examples/stereo_quick/inp/models.dat

@@ -0,0 +1,59 @@
+
+kin global
+    pressures = (
+        0.1  1.0  10.0 100.0
+    )
+    rate_temps = (
+        500. 600. 700. 800. 900. 1000.
+        1100. 1200. 1300. 1400. 1500
+        1600. 1700. 1800. 1900. 2000.
+    )
+    therm_temps = (
+        200. 300. 400. 500. 600. 700. 800. 900. 1000. 1100. 1200.
+        1300. 1400. 1500. 1600. 1700. 1800. 1900. 2000. 2100. 2200.
+        2300. 2400. 2500. 2600. 2700. 2800. 2900. 3000.
+    )
+    rate_fit = (
+        fit_method = plog
+        pdep_temps = [500.0, 1000.0]
+        pdep_tol = 20.0
+        pdep_pval = 1.0
+        pdep_plow = None
+        pdep_phigh = None
+        arrfit_dbltol = 15.0
+    )
+    therm_fit = (
+        ref_scheme = basic
+        ref_enes = Best
+    )
+end kin
+
+spc global
+    ene = (
+        lvl1 = dft
+    )
+    rot = (
+        mod = rigid
+    )
+    vib = (
+        mod = harm
+        geolvl = pm3
+        scale = on
+    )
+    tors = (
+        mod = rigid
+        enelvl = pm3
+        geolvl = pm3
+        scale = on
+    )
+    symm = (
+        mod = HCO_model
+        geolvl = pm3
+    )
+    ts = (
+        tunnel = eckart
+        sadpt = fixed
+        wells = fake
+        nobar = pst
+    )
+end spc

examples/stereo_quick/inp/run.dat

@@ -0,0 +1,38 @@
+
+input
+    run_prefix = ./run
+    save_prefix = ./save
+    canonical = True
+end input
+
+spc
+    # Runs canonical enantiomers *only*
+    1-6
+end spc
+
+pes
+    # Runs non-canonical enantiomers *only*
+    # (To verify that `canonical = True` is working)
+    1: 2
+end pes
+
+els
+    # No conformer sampling
+    spc init_geom   runlvl=pm3 inplvl=pm3
+    ts find_ts      runlvl=pm3 inplvl=pm3
+    all conf_hess   runlvl=pm3 inplvl=pm3
+    all conf_energy runlvl=dft  inplvl=pm3
+end els
+
+thermo
+    write_mess  kin_model=global spc_model=global cnf_range=min sort=freqs(pm3),sp(pm3),gibbs(700)
+    run_mess    kin_model=global spc_model=global cnf_range=min sort=freqs(pm3),sp(pm3),gibbs(700) nprocs=10
+    run_fits    kin_model=global spc_model=global cnf_range=min sort=freqs(pm3),sp(pm3),gibbs(700)
+end thermo
+
+ktp
+    write_mess  kin_model=global spc_model=global
+    run_mess    kin_model=global spc_model=global nprocs=10
+    run_fits    kin_model=global spc_model=global
+end ktp
+

examples/stereo_quick/inp/species.csv

@@ -0,0 +1,8 @@
+'name','smiles','inchi','inchikey','mult','charge','canon_enant_ich'
+'H2','[H][H]','InChI=1S/H2/h1H','UFHFLCQGNIYNRP-UHFFFAOYSA-N',1,0,'InChI=1S/H2/h1H'
+'CH4','C','InChI=1S/CH4/h1H4','VNWKTOKETHGBQD-UHFFFAOYSA-N',1,0,'InChI=1S/CH4/h1H4'
+'H2O','O','InChI=1S/H2O/h1H2','XLYOFNOQVPJJNP-UHFFFAOYSA-N',1,0,'InChI=1S/H2O/h1H2'
+'OH','[OH]','InChI=1S/HO/h1H','TUJKJAMUKRIRHC-UHFFFAOYSA-N','2','0','InChI=1S/HO/h1H'
+'C3o2','CC(C)O','InChI=1S/C3H8O/c1-3(2)4/h3-4H,1-2H3','KFZMGEQAYNKOFK-UHFFFAOYSA-N','1','0','InChI=1S/C3H8O/c1-3(2)4/h3-4H,1-2H3'
+'C3o2y1r0','[CH2][C@@H](C)O','InChI=1S/C3H7O/c1-3(2)4/h3-4H,1H2,2H3/t3-/m0/s1','INKFUXNIEHXFJX-VKHMYHEASA-N','2','0','InChI=1S/C3H7O/c1-3(2)4/h3-4H,1H2,2H3/t3-/m0/s1'
+'C3o2y1r1','[CH2][C@H](C)O','InChI=1S/C3H7O/c1-3(2)4/h3-4H,1H2,2H3/t3-/m1/s1','INKFUXNIEHXFJX-GSVOUGTGSA-N','2','0','InChI=1S/C3H7O/c1-3(2)4/h3-4H,1H2,2H3/t3-/m0/s1'

examples/stereo_quick/inp/theory.dat

@@ -0,0 +1,24 @@
+level pm3
+    method = pm3
+    orb_res = RU
+    program = gaussian16
+    mem = 1.0
+    nprocs = 1
+end level
+
+level pm6
+    method = pm6
+    orb_res = RU
+    program = gaussian16
+    mem = 1.0
+    nprocs = 1
+end level
+
+level dft
+    method = bp86
+    basis = def2-sv(p)
+    orb_res = RU
+    program = gaussian16
+    mem = 2.0
+    nprocs = 1
+end level

examples/ts_conf/.gitignore

@@ -0,0 +1,3 @@
+*
+!.gitignore
+!inp/

examples/ts_conf/inp/.gitignore

@@ -0,0 +1,8 @@
+*
+!.gitignore
+!inp/
+!mechanism.dat
+!models.dat
+!run.dat
+!species.csv
+!theory.dat

examples/ts_conf/inp/mechanism.dat

@@ -0,0 +1,5 @@
+REACTIONS    CAL/MOL   MOL
+
+CH4 + OH = CH3 + H2O              1.000      0.000      0.000         # pes.subpes.channel  1.1.1
+
+END

examples/ts_conf/inp/models.dat

@@ -0,0 +1,59 @@
+
+kin global
+    pressures = (
+        0.1  1.0  10.0 100.0
+    )
+    rate_temps = (
+        500. 600. 700. 800. 900. 1000.
+        1100. 1200. 1300. 1400. 1500
+        1600. 1700. 1800. 1900. 2000.
+    )
+    therm_temps = (
+        200. 300. 400. 500. 600. 700. 800. 900. 1000. 1100. 1200.
+        1300. 1400. 1500. 1600. 1700. 1800. 1900. 2000. 2100. 2200.
+        2300. 2400. 2500. 2600. 2700. 2800. 2900. 3000.
+    )
+    rate_fit = (
+        fit_method = plog
+        pdep_temps = [500.0, 1000.0]
+        pdep_tol = 20.0
+        pdep_pval = 1.0
+        pdep_plow = None
+        pdep_phigh = None
+        arrfit_dbltol = 15.0
+    )
+    therm_fit = (
+        ref_scheme = basic
+        ref_enes = Best
+    )
+end kin
+
+spc global
+    ene = (
+        lvl1 = dft
+    )
+    rot = (
+        mod = rigid
+    )
+    vib = (
+        mod = harm
+        geolvl = pm3
+        scale = on
+    )
+    tors = (
+        mod = 1dhrfa
+        enelvl = pm3
+        geolvl = pm3
+        scale = on
+    )
+    symm = (
+        mod = HCO_model
+        geolvl = pm3
+    )
+    ts = (
+        tunnel = eckart
+        sadpt = fixed
+        wells = fake
+        nobar = pst
+    )
+end spc

examples/ts_conf/inp/run.dat

@@ -0,0 +1,35 @@
+
+input
+    run_prefix = ./run
+    save_prefix = ./save
+end input
+
+spc
+    1-5
+end spc
+
+pes
+    1: 1
+end pes
+
+els
+    spc init_geom   runlvl=pm3 inplvl=pm3
+    ts find_ts      runlvl=pm3 inplvl=pm3
+    all conf_samp   runlvl=pm3 inplvl=pm3
+    all conf_hess   runlvl=pm3 inplvl=pm3 cnf_range=n100
+    all conf_energy runlvl=dft  inplvl=pm3 cnf_range=min sort=freqs(pm3),sp(pm3),gibbs(700)
+    all hr_scan     runlvl=pm3 inplvl=pm3 cnf_range=min sort=freqs(pm3),sp(pm3),gibbs(700) tors_model=1dhrfa
+end els
+
+thermo
+    write_mess  kin_model=global spc_model=global cnf_range=min sort=freqs(pm3),sp(pm3),gibbs(700)
+    run_mess    kin_model=global spc_model=global cnf_range=min sort=freqs(pm3),sp(pm3),gibbs(700) nprocs=10
+    run_fits    kin_model=global spc_model=global cnf_range=min sort=freqs(pm3),sp(pm3),gibbs(700)
+end thermo
+
+ktp
+    write_mess  kin_model=global spc_model=global
+    run_mess    kin_model=global spc_model=global nprocs=10
+    run_fits    kin_model=global spc_model=global
+end ktp
+

examples/ts_conf/inp/species.csv

@@ -0,0 +1,6 @@
+'name','smiles','inchi','inchikey','mult','charge','canon_enant_ich'
+'H2','[H][H]','InChI=1S/H2/h1H','UFHFLCQGNIYNRP-UHFFFAOYSA-N',1,0,'InChI=1S/H2/h1H'
+'OH','[OH]','InChI=1S/HO/h1H','TUJKJAMUKRIRHC-UHFFFAOYSA-N','2','0','InChI=1S/HO/h1H'
+'H2O','O','InChI=1S/H2O/h1H2','XLYOFNOQVPJJNP-UHFFFAOYSA-N','1','0','InChI=1S/H2O/h1H2'
+'CH3','[CH3]','InChI=1S/CH3/h1H3','WCYWZMWISLQXQU-UHFFFAOYSA-N','2','0','InChI=1S/CH3/h1H3'
+'CH4','C','InChI=1S/CH4/h1H4','VNWKTOKETHGBQD-UHFFFAOYSA-N','1','0','InChI=1S/CH4/h1H4'