Update dependencies

- remove dependency upper limits
- update poetry lockfile
- adapt to numpy 2.x (use np.round instead of np.round_)
- get rid of CI workflow interpolation step
- update pre-commit hooks

Author: greschd

.github/workflows_source/ci.yml

@@ -1,49 +1,31 @@
 repos:
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.15.2
+  rev: v3.19.1
   hooks:
     - id: pyupgrade
       args: [--py39-plus]
 - repo: https://github.com/psf/black
-  rev: 24.3.0
+  rev: 25.1.0
   hooks:
     - id: black
 - repo: https://github.com/pycqa/isort
-  rev: 5.13.2
+  rev: 6.0.0
   hooks:
   - id: isort
+- repo: https://github.com/python-poetry/poetry/
+  rev: "2.1.1"
+  hooks:
+    - id: poetry-check
+      name: "poetry: check pyproject.toml syntax"
+    - id: poetry-check
+      name: "poetry: check poetry.lock consistency"
+      args: ["--lock"]
+      files: '^(pyproject\.toml|poetry\.lock)$'
 - repo: local
   hooks:
-  - id: poetry-pyproject-check
-    name: "poetry: pyproject.toml check"
-    language: system
-    entry: poetry
-    args: ["check"]
-    files: '^(pyproject\.toml)$'
-    pass_filenames: false
-
-  - id: poetry-lockfile-consistency
-    name: "poetry: lockfile consistency check"
-    language: system
-    entry: poetry
-    args: ['lock', '--check']
-    files: '^(pyproject\.toml)|(poetry\.lock)$'
-    pass_filenames: false
-
   - id: pylint
     name: pylint
     entry: pylint
     language: system
     types: [python]
     exclude: '^(doc/)|(examples/)|(futures/)|(utils/)'
-
-  - id: interpolate-workflows
-    name: Interpolate Github workflows
-    entry: python ./utils/interpolate_yaml_anchors.py
-    language: system
-    files: |
-      (?x)^(
-        .github/(.)*|
-        utils/interpolate_yaml_anchors.py
-      )$
-    pass_filenames: false

.pre-commit-config.yaml

@@ -120,7 +120,6 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 html_theme = "sphinx_rtd_theme"
-html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the

doc/source/conf.py

@@ -2,11 +2,11 @@
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
 
-[tool.poetry]
+[project]
 name = "z2pack"
-version = "2.2.0"
-description = "Automating the computation of topological numbers of band-structures.."
-authors = ["Dominik Gresch <[email protected]>"]
+version = "2.2.1"
+description = "Automating the computation of topological numbers of band-structures."
+authors = [{ name ="Dominik Gresch", email = "[email protected]" }]
 license = "GPL"
 readme = "README.md"
 documentation = "https://z2pack.greschd.ch"
@@ -37,33 +37,30 @@ keywords = [
 packages = [
     { include = "z2pack", from = "src" },
 ]
+requires-python = ">=3.9"
+dependencies = [
+    "numpy>=1.20",
+    "scipy>=1.7",
+    "decorator>=5.0",
+    "blessings>=1.7",
+    "sortedcontainers>=2.4.0",
+    "msgpack>=1.0",
+    "fsc.locker>=1.1.0",
+    "fsc.formatting>=1.0.0",
+    "fsc.iohelper>=1.0.3",
+]
 
-[tool.poetry.dependencies]
-python = ">=3.9,<3.13"
-numpy = "^1.20"
-scipy = "^1.7"
-decorator = "^5.0"
-blessings = "^1.7"
-sortedcontainers = "^2.4.0"
-msgpack = "^1.0"
-"fsc.locker" = "^1.1.0"
-"fsc.formatting" = "^1.0.0"
-"fsc.iohelper" = "^1.0.3"
-matplotlib = { version = "^3", optional = true }
-tbmodels = { version =  "^1.1", optional = true }
+[project.optional-dependencies]
+plot = [ "matplotlib>=3" ]
+tb = [ "tbmodels>=1.1" ]
 
 [tool.poetry.group.dev.dependencies]
-sphinx = "^5"
-sphinx-rtd-theme = "^1.1.1"
-pytest = "^6"
-pytest-cov = "^4.0.0"
-pre-commit = "^3.0.0"
-pylint = "^3"
-"ruamel.yaml" = "^0.17"
-
-[tool.poetry.extras]
-plot = ["matplotlib"]
-tb = ["tbmodels"]
+sphinx = ">=5"
+sphinx-rtd-theme = ">=1.1.1"
+pytest = ">=6"
+pytest-cov = ">=4.0.0"
+pre-commit = ">=3.0.0"
+pylint = ">=3"
 
 [tool.black]
 line-length = 100
@@ -108,6 +105,7 @@ disable = [
     "consider-using-f-string",
     "use-dict-literal",
     "too-many-arguments",
+    "too-many-positional-arguments",
 ]
 
 [tool.pylint.design]

poetry.lock

@@ -45,7 +45,7 @@ def _check_dim(fct, kpt):
 def _check_closed(fct, kpt):
     """Checks whether the k-point list forms a closed loop."""
     delta = kpt[-1] - kpt[0]
-    if not np.isclose(np.round_(delta), delta).all():
+    if not np.isclose(np.round(delta), delta).all():
         raise ValueError("The k-point line does not form a closed loop.")
     return fct(kpt)
 
@@ -133,7 +133,7 @@ def wannier90_nnkpts(kpt):
     num_kpt = len(kpt) - 1
     bz_diff = [np.zeros(3, dtype=int) for _ in range(num_kpt - 1)]
     # check whether the last k-point is in a different UC
-    bz_diff.append(np.array(np.round_(kpt[-1] - kpt[0]), dtype=int))
+    bz_diff.append(np.array(np.round(kpt[-1] - kpt[0]), dtype=int))
     string = "begin nnkpts\n"
     for i, k in enumerate(bz_diff):
         j = (i + 1) % num_kpt

pyproject.toml

@@ -1,4 +1,4 @@
-""""Defines the result (data + convergence information) object for line calculations."""
+""" "Defines the result (data + convergence information) object for line calculations."""
 
 from .._result import Result
 

src/z2pack/fp/kpoint.py

@@ -114,7 +114,7 @@ def _run_line_impl(*controls, system, line, save_file=None, init_result=None, se
     """
     # check if the line function is closed (up to an inverse lattice vector)
     delta = np.array(line(1)) - np.array(line(0))
-    if not np.isclose(np.round_(delta), delta).all():
+    if not np.isclose(np.round(delta), delta).all():
         raise ValueError(
             "Start and end points of the line differ by {}, which is not an inverse lattice vector.".format(
                 delta

src/z2pack/line/_result.py

@@ -1,4 +1,4 @@
-""""Defines the result (data + convergence information) object for surface calculations."""
+""" "Defines the result (data + convergence information) object for surface calculations."""
 
 from .._result import Result
 

src/z2pack/line/_run.py

@@ -1,4 +1,4 @@
-""""Defines the result (data + convergence information) object for volume calculations."""
+""" "Defines the result (data + convergence information) object for volume calculations."""
 
 from .._result import Result