Development

.github/workflows/coverage.yml

@@ -35,6 +35,8 @@ concurrency:
 
 jobs:
   run-code-coverage:
+    # permissions:
+    #   contents: write
     environment:
       name: github-pages
       url: ${{ steps.deployment.outputs.page_url }} 
@@ -97,7 +99,7 @@ jobs:
           minColorRange: 0
 
       - name: upload artifact
-        uses: actions/upload-pages-artifact@v1
+        uses: actions/upload-pages-artifact@v3
         with: 
           path: './build/coverage/'
 
@@ -106,12 +108,11 @@ jobs:
         if: ${{ github.ref == 'refs/heads/main' }}
         uses: actions/deploy-pages@v2
         id: deployment
-        with:
-          path: './build/coverage/'  # Use the same coverage directory
 
-      - name: deploy to GitHub Pages (non-main branch)
-        if: ${{ github.ref != 'refs/heads/main' }}
-        uses: actions/deploy-pages@v2
-        with:
-          path: './build/coverage/'  # Same local coverage directory
-          branch: gh-pages-${{ github.head_ref }}  # Deploy to a branch-specific GitHub Pages branch
+      # - name: deploy to Github Pages (development branch)
+      #   if: ${{ github.ref != 'refs/heads/main' }}
+      #   uses: peaceiris/actions-gh-pages@v4
+      #   with:
+      #     publish_dir: ./build/coverage/
+      #     github_token: ${{ secrets.GITHUB_TOKEN }}
+      #     destination_dir: development-branch/

.github/workflows/python.yml

@@ -71,6 +71,7 @@ jobs:
           python --version
           python -m pip install pip-tools
           python -m pip install pytest
+          python -m pip install parameterized
           python -m piptools compile -o requirements.txt pyproject.toml --all-build-deps
           python -m pip install -r requirements.txt
 
@@ -79,7 +80,7 @@ jobs:
           cmake --version
           python --version
           ${{ env.FC }} --version
-          python -m pip install .
+          python -m pip install '.[ase]'
 
       - name: Test
         run: |

.gitignore

@@ -33,4 +33,19 @@ fort.*
 *.eps
 *.pyc
 *.xyz
-.coverage
+.coverage
+*CAR
+*.pckl
+.DS_Store
+fortranobject.c*
+*.db
+CHG
+EIGENVAL
+IBZKPT
+KPOINTS
+PCDAT
+REPORT
+vasprun.xml
+DVASP_MACE_comparison/
+pca_model*.pkl
+.benchmarks/

app/main.f90

@@ -11,7 +11,7 @@ program raffle_program
   use inputs
   use read_structures, only: get_gdfs_from_data
   use raffle, only: raffle_generator_type, distribs_container_type
-  use raffle__geom_rw, only: geom_read, geom_write
+  use raffle__geom_rw, only: geom_read, geom_write, basis_type
   implicit none
 
   ! Local variables
@@ -21,6 +21,7 @@ program raffle_program
   !! Buffer for strings
   character(:), allocatable :: next_dir
   !! Next directory name
+  type(basis_type) :: host
 
   real(real32), dimension(:), allocatable :: tmp_energies
   !! Temporary array for element energies
@@ -107,7 +108,8 @@ program raffle_program
   ! set the host structure
   !-----------------------------------------------------------------------------
   open(newunit=unit, file=filename_host, status='old')
-  call geom_read(unit, generator%host)
+  call geom_read(unit, host)
+  call generator%set_host(host)
   close(unit)
   if(grid_spacing.gt.1.E-6.and.all(grid.ne.0))then
      call stop_program('Cannot specify grid spacing and grid at the same time')

app/mod_read_structures.f90

@@ -132,6 +132,7 @@ function get_gdfs_from_data(input_dir, &
     ! read the structures from the list of files
     !---------------------------------------------------------------------------
     num_structures = 0
+    allocate(basis_list(0))
     do i = 1, size(structure_list)
        write(*,*) "Reading structure: ", trim(adjustl(structure_list(i)))
        select case(ifile_format)
@@ -184,7 +185,7 @@ function get_gdfs_from_data(input_dir, &
                        trim(basis%spec(j)%name), basis%spec(j)%num, &
                        j=1, basis%nspec &
                   )
-             call distribs_container%add(basis)
+             basis_list = [ basis_list, basis ]
           end do
           cycle
        end select

docs/requirements.txt

@@ -1,3 +1,3 @@
 sphinx==7.1.2
 sphinx-rtd-theme==1.3.0rc1
-f90wrap==0.2.16
+f90wrap==0.2.16

docs/source/install.rst

@@ -251,4 +251,4 @@ To test the installation of the Python library, navigate to the repository root
 
     pytest
 
-This will run the unit tests for the Python wrapper, as well as compile and run the Fortran unit tests.
+This will run the unit tests for the Python wrapper, as well as compile and run the Fortran unit tests.

docs/source/raffle.distributions.rst

@@ -0,0 +1,12 @@
+raffle.distributions module
+===========================
+
+.. .. automodule:: raffle.Raffle__Distribs_Container
+..    :members:
+..    :undoc-members:
+..    :show-inheritance:
+
+.. autoclass:: raffle.Raffle__Distribs_Container
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/raffle.generator.rst

@@ -0,0 +1,13 @@
+raffle.generator module
+=======================
+
+.. .. automodule:: raffle.Generator
+..    :members:
+..    :undoc-members:
+..    :show-inheritance:
+
+
+.. autoclass:: raffle.Generator
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/raffle.geom.rst

@@ -0,0 +1,12 @@
+raffle.geom_rw module
+=======================
+
+.. .. automodule:: raffle.Geom_Rw
+..    :members:
+..    :undoc-members:
+..    :show-inheritance:
+
+.. autoclass:: raffle.Geom_Rw
+   :members:
+   :undoc-members:
+   :show-inheritance: