DMA, Local force constants, Marcus dimension

.github/workflows/pythonapp.yml

@@ -7,21 +7,19 @@ on:
             - "examples/**"
             - "scripts/**"
             - "nix/**"
-            - "tests_staging/**"
-            - "deprecated/**"
     workflow_dispatch:
     schedule:
         - cron: '0 */12 * * *'
 jobs:
   buildNix:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: cachix/install-nix-action@v22
+      - uses: actions/checkout@v4
+      - uses: cachix/install-nix-action@v26
         with:
           nix_path: nixpkgs=channel:nixpkgs-unstable
           extra_nix_config: access-tokens = github.com=${{ secrets.GITHUB_TOKEN }}
-      - uses: cachix/cachix-action@v12
+      - uses: cachix/cachix-action@v14
         with:
           name: pysisyphus
           authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
@@ -32,15 +30,15 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/cache@v3
+    - uses: actions/checkout@v4
+    - uses: actions/cache@v4
       with:
         path: ~/.cache/pip
         key: ${{ runner.os }}-pip-
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.9.15
+        python-version: "3.12"
     - name: Upgrade pip
       run: |
         python -m pip install --upgrade pip
@@ -51,9 +49,9 @@ jobs:
       run: |
         pip install flake8
         # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --config flake8.ini
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --config flake8.ini
     - name: Install thermoanalysis
       run: |
         pip install git+https://github.com/eljost/thermoanalysis.git
@@ -64,12 +62,15 @@ jobs:
       run: >
         pytest -v
         --cov=pysisyphus --cov-config .coveragerc --cov-report xml --cov-report term
+        --color=yes
         --show-capture=no
         --durations=0
         -m "not benchmark and not skip_ci"
         tests
     - name: Upload coverage to codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         file: ./coverage.xml
         flags: unittests
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -169,6 +169,13 @@ pysisyphus/wavefunction/devel_ints/*
 version.py
 
 !tests/test_barriers/*.h5
+!tests/test_diabatization/00_bena2_cat/00_bena2_dcat.bson
+!tests/test_diabatization/00_bena2_cat/00_bena2_dcat.cis
+!tests/test_diabatization/00_bena2_cat/00_bena2_dcat.log
+!tests/test_dma/data/*
+!tests/test_es_capabilities/control_path_mult_*
+!tests/test_exc_densities/data/*
+!tests/test_rates/ethyl_propionate/*.h5
 !tests/test_franckcondon/*.h5
 !tests/test_franckcondon/naphthalene_gradient
 !tests/test_hessian_updates/*.h5
@@ -182,12 +189,18 @@ version.py
 !tests/test_orca/orca_tddft_triplets.out
 !tests/test_orca/fail_term.orca.out
 !tests/test_orca/orca_tddft_triplets.out
+!tests/test_orca/restricted.gbw
+!tests/test_orca/unrestricted.gbw
+!tests/test_openmolcas/butadien_vdzp.rasscf.h5
 !tests/test_openmolcas/cms_pdft_opt.yaml
-!tests/test_openmolcas/cms_pdft_opt.RasOrb
+!tests/test_openmolcas/cms_pdft.rasscf.h5
 !tests/test_point_charges/methane_control_path/*
 !tests/test_xtb/xtb_pass.out
 !tests/test_xtb/xtb_crash.out
+!tests/test_thermo/irc_*.orca.h5
+!tests/test_thermo/hcn_orca_b973c_hessian.h5
 !tests/test_turbomole/control_path_big_hess/*
+!tests/test_turbomole/make_dens/*/*
 !tests/test_tsopt/inp_hessian_ref.h5
 !tests/test_rates/peroxyl_r1_h5s/*.h5
 !tests/test_integrals/methane_def2svp_aomix.in
@@ -197,5 +210,12 @@ version.py
 !tests/test_wavefunction/pyrrole/*
 !tests/test_psf/step1_pdbreader.psf
 !tests/test_overlap_calculator/benzene/*
+!tests/test_local_force_constants/bf3_ccsd_t_ccpvdz.h5
 !tests/test_wavefunction/bases/*
+!tests/test_so_coupling/data/*
+!tests/test_turbomole/make_dens/*
+!tests/test_numerov/*.dat
+!tests/test_partfuncs/ts_final_hessian_xtb.h5
 !pysisyphus/wf_library/*
+!pysisyphus/numint/lebedev_grids_4pi.npz
+!pysisyphus/test_cos/multi_state_inp.npz

README.md

@@ -1,4 +1,4 @@
-![pysisyphus logo](resources/logo_small.png)
+![pysisyphus logo](resources/logo_new_cut_small.png)
 
 [![Documentation Status](https://readthedocs.org/projects/pysisyphus/badge/?version=master)](https://pysisyphus.readthedocs.io/en/master/?badge=master)
 [![build](https://github.com/eljost/pysisyphus/workflows/Python%20application/badge.svg)](https://github.com/eljost/pysisyphus/actions)