Pylint and Mypy fixes to solve CI errors. Remove Python 3.8 support (#…

…1374)

* Fixed pylint warnings

* Fixed mypy errors

* Fixed errors in tests due to old package networkx

* Copyright and style fixes

* Updated contribution guidelines

* Removed unused type ignore comment

* Added transpiler to pylintdict

* debug macos pipeline

* Test using macos 13

* Test with macos12

* Test setup conda

* Dropped python 3.9 support

* Copyright fix

* Added debug for psi4

* install libecpint for psi4 on ubuntu for python 3.9 and 3.10

* Sintax error fix

* Fixed logic for libecpint installation

* Removed python 3.8 folders

* Fixed mergify yml

* Added release note for python 3.8 drop

* Removed unnecessary package from requirements-decv

.github/actions/install-psi4/action.yml

@@ -1,6 +1,6 @@
 # This code is part of a Qiskit project.
 #
-# (C) Copyright IBM 2021, 2023.
+# (C) Copyright IBM 2021, 2025.
 #
 # This code is licensed under the Apache License, Version 2.0. You may
 # obtain a copy of this license in the LICENSE.txt file in the root directory
@@ -25,6 +25,11 @@ runs:
     - run : |
         source "$CONDA/etc/profile.d/conda.sh"
         conda activate psi4env
+        py_requires_libecpint=("3.9" "3.10")
+        if [[ "${{ inputs.os }}" == "ubuntu-latest" && " ${py_requires_libecpint[@]} " =~ "${{ inputs.python-version }}" ]]; then
+          echo "installs libecpint"
+          conda install -c conda-forge libecpint
+        fi
         echo "installs psi4 stable release"
         conda install -y psi4 python=${{ inputs.python-version }} -c conda-forge/label/libint_dev -c conda-forge
       shell: bash

.github/actions/run-tests/action.yml

@@ -38,7 +38,7 @@ runs:
         if [ "${{ inputs.event-name }}" == "schedule" ] || [ "${{ inputs.run-slow }}" == "true" ]; then
           export QISKIT_TESTS="run_slow"
         fi
-        if [ "${{ inputs.os }}" == "ubuntu-latest" ] && [ "${{ inputs.python-version }}" == "3.8" ]; then
+        if [ "${{ inputs.os }}" == "ubuntu-latest" ] && [ "${{ inputs.python-version }}" == "3.9" ]; then
           export PYTHON="coverage3 run --source qiskit_nature --omit */gauopen/* --parallel-mode"
         fi
         stestr --test-path test run 2> >(tee /dev/stderr out.txt > /dev/null)

.github/workflows/deploy-code.yml

@@ -25,7 +25,7 @@ jobs:
       id-token: write
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5

.github/workflows/deploy-docs.yml

@@ -25,7 +25,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
     steps:
       - uses: actions/checkout@v4
         with:

.github/workflows/main.yml

@@ -1,6 +1,6 @@
 # This code is part of a Qiskit project.
 #
-# (C) Copyright IBM 2021, 2024.
+# (C) Copyright IBM 2021, 2025.
 #
 # This code is licensed under the Apache License, Version 2.0. You may
 # obtain a copy of this license in the LICENSE.txt file in the root directory
@@ -36,7 +36,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.8]
+        python-version: [3.9]
     steps:
       - name: Print Concurrency Group
         env:
@@ -149,14 +149,14 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.8, 3.9, '3.10', 3.11, 3.12]
+        python-version: [3.9, '3.10', 3.11, 3.12]
         include:
           - os: macos-latest
-            python-version: 3.8
+            python-version: 3.9
           - os: macos-latest
             python-version: 3.12
           - os: windows-latest
-            python-version: 3.8
+            python-version: 3.9
           - os: windows-latest
             python-version: 3.12
     steps:
@@ -169,6 +169,12 @@ jobs:
             setup.py
             requirements.txt
             requirements-dev.txt
+      - uses: conda-incubator/setup-miniconda@v3
+        id: setup-miniforge
+        continue-on-error: true
+        with:
+          miniforge-version: latest
+        if: ${{ matrix.os == 'macos-latest' }}
       - name: Create conda environment
         run: |
           if [ "${{ matrix.os }}" == "macos-latest" ]; then
@@ -195,11 +201,6 @@ jobs:
       - uses: ./.github/actions/install-nature
         with:
           use-conda: "true"
-      - name: Set up problem matches
-        run: |
-          echo "::add-matcher::./.github/problem_matchers/pylint.json"
-          echo "::add-matcher::./.github/problem_matchers/mypy.json"
-        if: ${{ matrix.os == 'ubuntu-latest' && matrix.python-version == 3.8 }}
       - name: Run lint
         run: |
           source "$CONDA/etc/profile.d/conda.sh"
@@ -245,7 +246,7 @@ jobs:
           conda activate psi4env
           coverage3 combine
           mv .coverage ./ci-artifact-data/nat.dat
-        if: ${{ matrix.os == 'ubuntu-latest' && matrix.python-version == 3.8 }}
+        if: ${{ matrix.os == 'ubuntu-latest' && matrix.python-version == 3.9 }}
         shell: bash
       - uses: actions/upload-artifact@v4
         with:
@@ -274,7 +275,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.8, 3.12]
+        python-version: [3.9, 3.12]
     steps:
       - uses: actions/checkout@v4
         with:
@@ -341,30 +342,26 @@ jobs:
           cd docs/_build/html
           mkdir artifacts
           tar -zcvf artifacts/tutorials.tar.gz --exclude=./artifacts .
-        if: ${{ matrix.python-version == 3.8 && !startsWith(github.ref, 'refs/heads/stable') && !startsWith(github.base_ref, 'stable/') }}
+        if: ${{ matrix.python-version == 3.9 && !startsWith(github.ref, 'refs/heads/stable') && !startsWith(github.base_ref, 'stable/') }}
         shell: bash
       - name: Run upload stable tutorials
         uses: actions/upload-artifact@v4
         with:
           name: tutorials-stable${{ matrix.python-version }}
           path: docs/_build/html/artifacts/tutorials.tar.gz
-        if: ${{ matrix.python-version == 3.8 && !startsWith(github.ref, 'refs/heads/stable') && !startsWith(github.base_ref, 'stable/') }}
+        if: ${{ matrix.python-version == 3.9 && !startsWith(github.ref, 'refs/heads/stable') && !startsWith(github.base_ref, 'stable/') }}
   Deprecation_Messages_and_Coverage:
     if: github.repository_owner == 'qiskit-community'
     needs: [Checks, Nature, Tutorials]
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - uses: actions/download-artifact@v4
-        with:
-          name: ubuntu-latest-3.8
-          path: /tmp/u38
       - uses: actions/download-artifact@v4
         with:
           name: ubuntu-latest-3.9
@@ -383,16 +380,16 @@ jobs:
           path: /tmp/u312
       - uses: actions/download-artifact@v4
         with:
-          name: macos-latest-3.8
-          path: /tmp/m38
+          name: macos-latest-3.9
+          path: /tmp/m39
       - uses: actions/download-artifact@v4
         with:
           name: macos-latest-3.12
           path: /tmp/m312
       - uses: actions/download-artifact@v4
         with:
-          name: windows-latest-3.8
-          path: /tmp/w38
+          name: windows-latest-3.9
+          path: /tmp/w39
       - uses: actions/download-artifact@v4
         with:
           name: windows-latest-3.12
@@ -402,10 +399,10 @@ jobs:
         shell: bash
       - name: Combined Deprecation Messages
         run: |
-          sort -f -u /tmp/u38/nat.dep /tmp/u39/nat.dep /tmp/u310/nat.dep /tmp/u311/nat.dep /tmp/u312/nat.dep /tmp/m38/nat.dep /tmp/m312/nat.dep /tmp/w38/nat.dep /tmp/w312/nat.dep || true
+          sort -f -u /tmp/u39/nat.dep /tmp/u310/nat.dep /tmp/u311/nat.dep /tmp/u312/nat.dep /tmp/m39/nat.dep /tmp/m312/nat.dep /tmp/w39/nat.dep /tmp/w312/nat.dep || true
         shell: bash
       - name: Coverage combine
-        run: coverage3 combine /tmp/u38/nat.dat
+        run: coverage3 combine /tmp/u39/nat.dat
         shell: bash
       - name: Upload to Coveralls
         env:

.mergify.yml

@@ -1,19 +1,19 @@
 queue_rules:
   - name: automerge
-    conditions:
-      - check-success=Deprecation_Messages_and_Coverage (3.8)
+    queue_conditions:
+      - check-success=Deprecation_Messages_and_Coverage (3.9)
+    merge_method: squash
 
 pull_request_rules:
   - name: automatic merge on CI success and review
     conditions:
-      - check-success=Deprecation_Messages_and_Coverage (3.8)
+      - check-success=Deprecation_Messages_and_Coverage (3.9)
       - "#approved-reviews-by>=1"
       - label=automerge
       - label!=on hold
     actions:
       queue:
         name: automerge
-        method: squash
   - name: backport
     conditions:
       - label=stable backport potential

.pylintdict

@@ -598,6 +598,7 @@ tran
 translational
 transpilation
 transpile
+transpiler
 trotterization
 tryptophan
 tuple

CONTRIBUTING.md

@@ -80,8 +80,9 @@ please ensure that:
    that change and that the PR is tagged for the changelog.
 
 5. Ensure all code, including unit tests, has the copyright header. The copyright
-   date will be checked by CI build. The format of the date(s) is _year of creation,
-   last year changed_. So for example:
+   date will be checked by CI build. You can automatically fix the copyright dates
+   by running `make copyright`.
+   The format of the date(s) is _year of creation, last year changed_. So for example:
 
    > \# (C) Copyright IBM 2018, 2021.
 

qiskit_nature/second_q/algorithms/excited_states_solvers/qeom.py

@@ -1,6 +1,6 @@
 # This code is part of a Qiskit project.
 #
-# (C) Copyright IBM 2020, 2024.
+# (C) Copyright IBM 2020, 2025.
 #
 # This code is licensed under the Apache License, Version 2.0. You may
 # obtain a copy of this license in the LICENSE.txt file in the root directory
@@ -946,6 +946,7 @@ def _evaluate_observables_excited_states(
 
         return aux_operators_eigenvalues, transition_amplitudes
 
+    # pylint: disable=too-many-positional-arguments
     def _build_qeom_result(
         self,
         problem,

qiskit_nature/second_q/circuit/library/ansatzes/ucc.py

@@ -1,6 +1,6 @@
 # This code is part of a Qiskit project.
 #
-# (C) Copyright IBM 2021, 2024.
+# (C) Copyright IBM 2021, 2025.
 #
 # This code is licensed under the Apache License, Version 2.0. You may
 # obtain a copy of this license in the LICENSE.txt file in the root directory
@@ -18,7 +18,7 @@
 import logging
 from functools import partial
 from itertools import chain
-from typing import Callable, Sequence
+from typing import Callable, Sequence, Dict, Any
 
 from qiskit.circuit import QuantumCircuit
 from qiskit.circuit.library import EvolvedOperatorAnsatz
@@ -456,12 +456,14 @@ def _get_excitation_generators(self) -> list[Callable]:
         logger.debug("Gathering excitation generators...")
         generators: list[Callable] = []
 
-        extra_kwargs = {
-            "alpha_spin": self._alpha_spin,
-            "beta_spin": self._beta_spin,
-            "max_spin_excitation": self._max_spin_excitation,
-            "generalized": self._generalized,
-            "preserve_spin": self._preserve_spin,
+        extra_kwargs: Dict[str, Any] = {
+            "alpha_spin": bool(self._alpha_spin),
+            "beta_spin": bool(self._beta_spin),
+            "max_spin_excitation": (
+                int(self._max_spin_excitation) if self._max_spin_excitation is not None else None
+            ),
+            "generalized": bool(self._generalized),
+            "preserve_spin": bool(self._preserve_spin),
         }
 
         if isinstance(self.excitations, str):
@@ -480,9 +482,11 @@ def _get_excitation_generators(self) -> list[Callable]:
                 )
             )
         elif isinstance(self.excitations, list):
-            for exc in self.excitations:  # type: ignore
+            for excitation in self.excitations:
                 generators.append(
-                    partial(generate_fermionic_excitations, num_excitations=exc, **extra_kwargs)
+                    partial(
+                        generate_fermionic_excitations, num_excitations=excitation, **extra_kwargs
+                    )
                 )
         elif callable(self.excitations):
             generators = [self.excitations]

qiskit_nature/second_q/circuit/library/ansatzes/uvcc.py

@@ -1,6 +1,6 @@
 # This code is part of a Qiskit project.
 #
-# (C) Copyright IBM 2021, 2024.
+# (C) Copyright IBM 2021, 2025.
 #
 # This code is licensed under the Apache License, Version 2.0. You may
 # obtain a copy of this license in the LICENSE.txt file in the root directory
@@ -322,11 +322,11 @@ def _get_excitation_generators(self) -> list[Callable]:
                 )
             )
         elif isinstance(self.excitations, list):
-            for exc in self.excitations:  # type: ignore
+            for excitation in self.excitations:
                 generators.append(
                     partial(
                         generate_vibration_excitations,
-                        num_excitations=exc,
+                        num_excitations=excitation,
                     )
                 )
         elif callable(self.excitations):

qiskit_nature/second_q/circuit/library/initial_states/hartree_fock.py

@@ -1,6 +1,6 @@
 # This code is part of a Qiskit project.
 #
-# (C) Copyright IBM 2018, 2023.
+# (C) Copyright IBM 2018, 2025.
 #
 # This code is licensed under the Apache License, Version 2.0. You may
 # obtain a copy of this license in the LICENSE.txt file in the root directory
@@ -269,8 +269,8 @@ def hartree_fock_bitstring(num_spatial_orbitals: int, num_particles: tuple[int,
         raise ValueError("# of particles must be less than or equal to # of orbitals.")
 
     half_orbitals = num_spatial_orbitals
-    bitstr = np.zeros(2 * num_spatial_orbitals, bool)
+    bitstr = np.zeros(2 * num_spatial_orbitals, dtype=bool)
     bitstr[:num_alpha] = True
     bitstr[half_orbitals : (half_orbitals + num_beta)] = True
 
-    return bitstr.tolist()
+    return [bool(x) for x in bitstr.tolist()]

qiskit_nature/second_q/circuit/library/initial_states/vscf.py

@@ -1,6 +1,6 @@
 # This code is part of a Qiskit project.
 #
-# (C) Copyright IBM 2020, 2023.
+# (C) Copyright IBM 2020, 2025.
 #
 # This code is licensed under the Apache License, Version 2.0. You may
 # obtain a copy of this license in the LICENSE.txt file in the root directory
@@ -16,6 +16,7 @@
 
 import logging
 
+from typing import List
 import numpy as np
 
 from qiskit import QuantumRegister
@@ -208,7 +209,7 @@ def vscf_bitstring_mapped(
     return bits
 
 
-def vscf_bitstring(num_modals: list[int]) -> list[bool]:
+def vscf_bitstring(num_modals: List[int]) -> List[bool]:
     """Compute the bitstring representing the VSCF initial state based on the modals per mode.
 
     Args:
@@ -219,10 +220,10 @@ def vscf_bitstring(num_modals: list[int]) -> list[bool]:
         The bitstring representing the state of the VSCF state as array of bools.
     """
     num_qubits = sum(num_modals)
-    bitstr = np.zeros(num_qubits, bool)
+    bitstr = np.zeros(num_qubits, dtype=bool)
     count = 0
     for modal in num_modals:
         bitstr[count] = True
         count += modal
 
-    return bitstr.tolist()
+    return [bool(x) for x in bitstr.tolist()]

qiskit_nature/second_q/drivers/psi4d/psi4driver.py

@@ -1,6 +1,6 @@
 # This code is part of a Qiskit project.
 #
-# (C) Copyright IBM 2018, 2024.
+# (C) Copyright IBM 2018, 2025.
 #
 # This code is licensed under the Apache License, Version 2.0. You may
 # obtain a copy of this license in the LICENSE.txt file in the root directory
@@ -245,5 +245,5 @@ def _run_psi4(input_file, output_file):
                     logger.error(line)
                     errmsg += line + "\n"
             raise QiskitNatureError(
-                f"{_optionals.PSI4} process return code {process.returncode}\n{errmsg}"
+                f"{_optionals.PSI4} process return code {process.returncode}: {errmsg}"
             )