Merge branch 'master' into bootstrap

.github/workflows/ci.yaml

@@ -15,13 +15,17 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - {python-version: "3.9", os: ubuntu-latest, documentation: True}
-          - {python-version: "3.10", os: ubuntu-latest, documentation: False}
-          - {python-version: "3.11", os: ubuntu-latest, documentation: False}
-          - {python-version: "3.12", os: ubuntu-latest, documentation: False}
+          - {python-version: "3.9", os: ubuntu-latest, documentation: True, coverage: True}
+          - {python-version: "3.10", os: ubuntu-latest, documentation: False, coverage: True}
+          - {python-version: "3.11", os: ubuntu-latest, documentation: False, coverage: True}
+          - {python-version: "3.12", os: ubuntu-latest, documentation: False, coverage: False}
 
     steps:
       - uses: actions/checkout@v2
+      - uses: actions/cache@v2
+        with:
+          key: ${{ github.ref }}
+          path: .cache
       - name: Set up python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
         with:
@@ -39,12 +43,22 @@ jobs:
           python -m isort ebcc/ --diff --check-only --verbose
           python -m flake8 ebcc/ --verbose
           python -m mypy ebcc/ --verbose
-      - name: Run unit tests
+      - name: Run unit tests with coverage
         run: |
           python -m pip install pytest pytest-cov
           pytest --cov ebcc/
+        if: matrix.coverage
+      - name: Run unit tests
+        run: |
+          python -m pip install pytest
+          pytest
+        if: ${{ ! matrix.coverage }}
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           verbose: true
+        if: matrix.coverage
+      - name: Deploy documentation
+        run: mkdocs gh-deploy --force -f docs/mkdocs.yaml
+        if: matrix.documentation && github.ref == 'refs/heads/master'

docs/features.md

@@ -0,0 +1,4 @@
+{%
+   include-markdown "../FEATURES.md"
+%}
+

docs/gen_files.py

@@ -0,0 +1,28 @@
+"""
+Generate the code reference pages.
+"""
+
+from pathlib import Path
+
+import mkdocs_gen_files
+
+
+for path in sorted(Path("ebcc").rglob("*.py")):
+    module_path = path.relative_to("ebcc").with_suffix("")
+    doc_path = path.relative_to("ebcc").with_suffix(".md")
+    full_doc_path = Path("reference", doc_path)
+    parts = ["ebcc", *module_path.parts]
+
+    if parts[-1] == "__init__":
+        parts = parts[:-1]
+        doc_path = doc_path.with_name("index.md")
+        full_doc_path = full_doc_path.with_name("index.md")
+
+    if not len(parts) or parts[-1] == "__main__" or parts[0] == "codegen":
+        continue
+
+    with mkdocs_gen_files.open(full_doc_path, "w") as fd:
+        identifier = ".".join(parts)
+        fd.write("::: " + identifier + "\n")
+
+    mkdocs_gen_files.set_edit_path(full_doc_path, path)

docs/index.md

@@ -0,0 +1,3 @@
+{%
+   include-markdown "../README.md"
+%}

docs/mkdocs.yaml

@@ -0,0 +1,71 @@
+site_name: ebcc
+
+watch:
+- ../ebcc
+
+theme:
+  name: readthedocs
+
+docs_dir: .
+
+site_dir: ../site
+
+plugins:
+- search
+- gen-files:
+    scripts:
+    - gen_files.py
+- section-index
+- include-markdown
+- mkdocstrings:
+    default_handler: python
+    handlers:
+        python:
+            rendering:
+                show_source: false
+            options:
+                docstring_style: google
+                members_order: source
+                line_length: 100
+                merge_init_into_class: true
+                show_if_no_docstring: false
+                show_root_members_full_path: true
+                show_object_full_path: true
+
+nav:
+- Home: "index.md"
+- Features: "features.md"
+- Code Reference:
+  - Coupled cluster:
+    - Restricted: reference/cc/rebcc.md
+    - Unrestricted: reference/cc/uebcc.md
+    - Generalised: reference/cc/gebcc.md
+    - Base: reference/cc/base.md
+  - Equation of motion:
+    - Restricted: reference/eom/reom.md
+    - Unrestricted: reference/eom/ueom.md
+    - Generalised: reference/eom/geom.md
+    - Base: reference/eom/base.md
+  - Orbital optimisation:
+    - Brueckner:
+      - Restricted: reference/opt/rbrueckner.md
+      - Unrestricted: reference/opt/ubrueckner.md
+      - Generalised: reference/opt/gbrueckner.md
+    - Base: reference/opt/base.md
+  - Core:
+    - Ansatz: reference/core/ansatz.md
+    - Damping: reference/core/damping.md
+    - Dumping: reference/core/dump.md
+    - Logging: reference/core/logging.md
+    - Precision: reference/core/precision.md
+  - Hamiltonian:
+    - Space: reference/ham/space.md
+    - Fock: reference/ham/fock.md
+    - ERIs: reference/ham/eris.md
+    - CDERIs: reference/ham/cderis.md
+    - Bosonic: reference/ham/elbos.md
+    - Base: reference/ham/base.md
+  - Utility:
+    - Permutations: reference/util/permutations.md
+    - Einstein summations: reference/util/einsumfunc.md
+    - Miscellaneous: reference/util/misc.md

ebcc/cc/base.py

@@ -60,19 +60,7 @@ class BaseOptions:
 
 
 class BaseEBCC(ABC):
-    """Base class for electron-boson coupled cluster.
-
-    Attributes:
-        mf: PySCF mean-field object.
-        log: Log to write output to.
-        options: Options for the EBCC calculation.
-        e_corr: Correlation energy.
-        amplitudes: Cluster amplitudes.
-        converged: Convergence flag.
-        lambdas: Cluster lambda amplitudes.
-        converged_lambda: Lambda convergence flag.
-        name: Name of the method.
-    """
+    """Base class for electron-boson coupled cluster."""
 
     # Types
     Options: type[BaseOptions] = BaseOptions
@@ -875,156 +863,6 @@ def hbar_matvec_ee(
         res = util.Namespace(**{key.rstrip("new"): val for key, val in res.items()})
         return res
 
-    def make_ip_mom_bras(
-        self,
-        eris: Optional[ERIsInputType] = None,
-        amplitudes: Optional[Namespace[SpinArrayType]] = None,
-        lambdas: Optional[Namespace[SpinArrayType]] = None,
-    ) -> tuple[SpinArrayType, ...]:
-        """Get the bra vectors to construct IP-EOM moments.
-
-        Args:
-            eris: Electron repulsion integrals.
-            amplitudes: Cluster amplitudes.
-            lambdas: Cluster lambda amplitudes.
-
-        Returns:
-            Bra vectors for IP-EOM moments.
-        """
-        func, kwargs = self._load_function(
-            "make_ip_mom_bras",
-            eris=eris,
-            amplitudes=amplitudes,
-            lambdas=lambdas,
-        )
-        res: tuple[SpinArrayType, ...] = func(**kwargs)
-        return res
-
-    def make_ea_mom_bras(
-        self,
-        eris: Optional[ERIsInputType] = None,
-        amplitudes: Optional[Namespace[SpinArrayType]] = None,
-        lambdas: Optional[Namespace[SpinArrayType]] = None,
-    ) -> tuple[SpinArrayType, ...]:
-        """Get the bra vectors to construct EA-EOM moments.
-
-        Args:
-            eris: Electron repulsion integrals.
-            amplitudes: Cluster amplitudes.
-            lambdas: Cluster lambda amplitudes.
-
-        Returns:
-            Bra vectors for EA-EOM moments.
-        """
-        func, kwargs = self._load_function(
-            "make_ea_mom_bras",
-            eris=eris,
-            amplitudes=amplitudes,
-            lambdas=lambdas,
-        )
-        res: tuple[SpinArrayType, ...] = func(**kwargs)
-        return res
-
-    def make_ee_mom_bras(
-        self,
-        eris: Optional[ERIsInputType] = None,
-        amplitudes: Optional[Namespace[SpinArrayType]] = None,
-        lambdas: Optional[Namespace[SpinArrayType]] = None,
-    ) -> tuple[SpinArrayType, ...]:
-        """Get the bra vectors to construct EE-EOM moments.
-
-        Args:
-            eris: Electron repulsion integrals.
-            amplitudes: Cluster amplitudes.
-            lambdas: Cluster lambda amplitudes.
-
-        Returns:
-            Bra vectors for EE-EOM moments.
-        """
-        func, kwargs = self._load_function(
-            "make_ee_mom_bras",
-            eris=eris,
-            amplitudes=amplitudes,
-            lambdas=lambdas,
-        )
-        res: tuple[SpinArrayType, ...] = func(**kwargs)
-        return res
-
-    def make_ip_mom_kets(
-        self,
-        eris: Optional[ERIsInputType] = None,
-        amplitudes: Optional[Namespace[SpinArrayType]] = None,
-        lambdas: Optional[Namespace[SpinArrayType]] = None,
-    ) -> tuple[SpinArrayType, ...]:
-        """Get the ket vectors to construct IP-EOM moments.
-
-        Args:
-            eris: Electron repulsion integrals.
-            amplitudes: Cluster amplitudes.
-            lambdas: Cluster lambda amplitudes.
-
-        Returns:
-            Ket vectors for IP-EOM moments.
-        """
-        func, kwargs = self._load_function(
-            "make_ip_mom_kets",
-            eris=eris,
-            amplitudes=amplitudes,
-            lambdas=lambdas,
-        )
-        res: tuple[SpinArrayType, ...] = func(**kwargs)
-        return res
-
-    def make_ea_mom_kets(
-        self,
-        eris: Optional[ERIsInputType] = None,
-        amplitudes: Optional[Namespace[SpinArrayType]] = None,
-        lambdas: Optional[Namespace[SpinArrayType]] = None,
-    ) -> tuple[SpinArrayType, ...]:
-        """Get the ket vectors to construct EA-EOM moments.
-
-        Args:
-            eris: Electron repulsion integrals.
-            amplitudes: Cluster amplitudes.
-            lambdas: Cluster lambda amplitudes.
-
-        Returns:
-            Ket vectors for EA-EOM moments.
-        """
-        func, kwargs = self._load_function(
-            "make_ea_mom_kets",
-            eris=eris,
-            amplitudes=amplitudes,
-            lambdas=lambdas,
-        )
-        res: tuple[SpinArrayType, ...] = func(**kwargs)
-        return res
-
-    def make_ee_mom_kets(
-        self,
-        eris: Optional[ERIsInputType] = None,
-        amplitudes: Optional[Namespace[SpinArrayType]] = None,
-        lambdas: Optional[Namespace[SpinArrayType]] = None,
-    ) -> tuple[SpinArrayType, ...]:
-        """Get the ket vectors to construct EE-EOM moments.
-
-        Args:
-            eris: Electron repulsion integrals.
-            amplitudes: Cluster amplitudes.
-            lambdas: Cluster lambda amplitudes.
-
-        Returns:
-            Ket vectors for EE-EOM moments.
-        """
-        func, kwargs = self._load_function(
-            "make_ee_mom_kets",
-            eris=eris,
-            amplitudes=amplitudes,
-            lambdas=lambdas,
-        )
-        res: tuple[SpinArrayType, ...] = func(**kwargs)
-        return res
-
     @abstractmethod
     def energy_sum(self, *args: str, signs_dict: Optional[dict[str, str]] = None) -> NDArray[float]:
         """Get a direct sum of energies.

ebcc/cc/gebcc.py

@@ -33,19 +33,7 @@
 
 
 class GEBCC(BaseEBCC):
-    """Restricted electron-boson coupled cluster.
-
-    Attributes:
-        mf: PySCF mean-field object.
-        log: Log to write output to.
-        options: Options for the EBCC calculation.
-        e_corr: Correlation energy.
-        amplitudes: Cluster amplitudes.
-        converged: Convergence flag.
-        lambdas: Cluster lambda amplitudes.
-        converged_lambda: Lambda convergence flag.
-        name: Name of the method.
-    """
+    """Restricted electron-boson coupled cluster."""
 
     # Types
     ERIs = GERIs

ebcc/cc/rebcc.py

@@ -29,19 +29,7 @@
 
 
 class REBCC(BaseEBCC):
-    """Restricted electron-boson coupled cluster.
-
-    Attributes:
-        mf: PySCF mean-field object.
-        log: Log to write output to.
-        options: Options for the EBCC calculation.
-        e_corr: Correlation energy.
-        amplitudes: Cluster amplitudes.
-        converged: Convergence flag.
-        lambdas: Cluster lambda amplitudes.
-        converged_lambda: Lambda convergence flag.
-        name: Name of the method.
-    """
+    """Restricted electron-boson coupled cluster."""
 
     # Types
     ERIs = RERIs

ebcc/cc/uebcc.py

@@ -31,19 +31,7 @@
 
 
 class UEBCC(BaseEBCC):
-    """Unrestricted electron-boson coupled cluster.
-
-    Attributes:
-        mf: PySCF mean-field object.
-        log: Log to write output to.
-        options: Options for the EBCC calculation.
-        e_corr: Correlation energy.
-        amplitudes: Cluster amplitudes.
-        converged: Convergence flag.
-        lambdas: Cluster lambda amplitudes.
-        converged_lambda: Lambda convergence flag.
-        name: Name of the method.
-    """
+    """Unrestricted electron-boson coupled cluster."""
 
     # Types
     ERIs = UERIs