Replace HTTP URLs with HTTPS, avoid from pytest import raises/mark

ADMIN.md

@@ -16,7 +16,7 @@ The general procedure for releasing `pymatgen` comprises the following steps:
 
 ## Initial setup
 
-Pymatgen uses [invoke](http://pyinvoke.org) to automate releases.
+Pymatgen uses [invoke](https://pyinvoke.org) to automate releases.
 You will also need `sphinx` and `doc2dash`.
 
 ```sh

CITATION.cff

@@ -5,7 +5,7 @@ message: |
 
   In addition, some of pymatgen's functionality is based on scientific advances
   / principles developed by the computational materials scientists in our team.
-  Please refer to pymatgen's docs at http://pymatgen.org on how to cite them.
+  Please refer to pymatgen's docs at https://pymatgen.org on how to cite them.
 authors:
 - family-names: Ong
   given-names: Shyue Ping

dev_scripts/nist_codata.txt

@@ -2,7 +2,7 @@
              Fundamental Physical Constants --- Complete Listing
 
 
-  From:  http://physics.nist.gov/constants
+  From:  https://physics.nist.gov/cuu/Constants/index.html
 
 
 

pyproject.toml

@@ -93,7 +93,7 @@ abinit = ["netcdf4>=1.7.1"]
 mlp = ["chgnet>=0.3.8", "matgl>=1.1.1"]
 electronic_structure = ["fdint>=2.0.2"]
 ci = ["pytest-cov>=4", "pytest-split>=0.8", "pytest>=8"]
-docs = ["sphinx", "sphinx_rtd_theme"]
+docs = ["invoke", "sphinx", "sphinx_rtd_theme", "sphinx_markdown_builder"]
 optional = [
     "ase>=3.23.0",
     # TODO: uv cannot install BoltzTraP2

src/pymatgen/alchemy/materials.py

@@ -369,7 +369,7 @@ def to_snl(self, authors: list[str], **kwargs) -> StructureNL:
             history += [
                 {
                     "name": snl_metadata.pop("name", "pymatgen"),
-                    "url": snl_metadata.pop("url", "http://pypi.python.org/pypi/pymatgen"),
+                    "url": snl_metadata.pop("url", "https://pypi.python.org/pypi/pymatgen"),
                     "description": hist,
                 }
             ]

src/pymatgen/analysis/bonds_jmol_ob.yaml

@@ -1,7 +1,7 @@
 # Default bond distances (when charge is unknown) from JMol.
 # As per JMol docs:
 # "Values taken from OpenBabel.
-# http://sourceforge.net/p/openbabel/code/485/tree/openbabel/trunk/data/element.txt (dated 10/20/2004)
+# https://sourceforge.net/p/openbabel/code/485/tree/openbabel/trunk/data/element.txt (dated 10/20/2004)
 # These values are a mix of common ion (Ba2+, Na+) distances and covalent distances."
 
 Ac: 1.88

src/pymatgen/analysis/local_env.py

@@ -1406,7 +1406,7 @@ class OpenBabelNN(NearNeighbors):
     @requires(
         openbabel,
         "BabelMolAdaptor requires openbabel to be installed with "
-        "Python bindings. Please get it at http://openbabel.org "
+        "Python bindings. Please get it at https://openbabel.org "
         "(version >=3.0.0).",
     )
     def __init__(self, order=True) -> None:

src/pymatgen/analysis/molecule_matcher.py

@@ -567,7 +567,7 @@ class MoleculeMatcher(MSONable):
     @requires(
         openbabel,
         "BabelMolAdaptor requires openbabel to be installed with Python "
-        "bindings. Please get it at http://openbabel.org (version >=3.0.0).",
+        "bindings. Please get it at https://openbabel.org (version >=3.0.0).",
     )
     def __init__(self, tolerance: float = 0.01, mapper=None) -> None:
         """
@@ -798,7 +798,7 @@ def kabsch(P: np.ndarray, Q: np.ndarray):
         P and Q, centered around the their centroid.
 
         For more info see:
-        - http://wikipedia.org/wiki/Kabsch_algorithm and
+        - https://wikipedia.org/wiki/Kabsch_algorithm and
         - https://cnx.org/contents/HV-RsdwL@23/Molecular-Distance-Measures
 
         Args:

src/pymatgen/analysis/wulff.py

@@ -102,7 +102,7 @@ class WulffShape:
 
     Wulff shape is the convex hull.
     Based on:
-    http://scipy.github.io/devdocs/generated/scipy.spatial.ConvexHull.html
+    https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.ConvexHull.html
 
     Process:
         1. get Wulff simplices

src/pymatgen/cli/pmg_config.py

@@ -199,7 +199,7 @@ def build_bader(fortran_command="gfortran"):
     Args:
         fortran_command: The Fortran compiler command.
     """
-    bader_url = "http://theory.cm.utexas.edu/henkelman/code/bader/download/bader.tar.gz"
+    bader_url = "https://theory.cm.utexas.edu/henkelman/code/bader/download/bader.tar.gz"
     cwd = os.getcwd()
     state = True
     try:

src/pymatgen/command_line/bader_caller.py

@@ -2,7 +2,7 @@
 Fortran code for calculating a Bader charge analysis.
 
 This module depends on a compiled bader executable available in the path.
-Please download the library at http://theory.cm.utexas.edu/henkelman/code/bader/
+Please download the library at https://theory.cm.utexas.edu/henkelman/code/bader/
 and follow the instructions to compile the executable.
 
 If you use this module, please cite:

src/pymatgen/core/operations.py

@@ -27,7 +27,7 @@
 class SymmOp(MSONable):
     """A symmetry operation in Cartesian space. Consists of a rotation plus a
     translation. Implementation is as an affine transformation matrix of rank 4
-    for efficiency. Read: http://wikipedia.org/wiki/Affine_transformation.
+    for efficiency. Read: https://wikipedia.org/wiki/Affine_transformation.
 
     Attributes:
         affine_matrix (np.ndarray): A 4x4 array representing the symmetry operation.

src/pymatgen/core/periodic_table.py

@@ -86,7 +86,7 @@ def __init__(self, symbol: SpeciesLike) -> None:
             long_name (str): Long name for element. e.g. "Hydrogen".
             A (int) : Atomic mass number (number of protons plus neutrons).
             atomic_radius_calculated (float): Calculated atomic radius for the element. This is the empirical value.
-                Data is obtained from http://wikipedia.org/wiki/Atomic_radii_of_the_elements_(data_page).
+                Data is obtained from https://wikipedia.org/wiki/Atomic_radii_of_the_elements_(data_page).
             van_der_waals_radius (float): Van der Waals radius for the element. This is the empirical value determined
                 from critical reviews of X-ray diffraction, gas kinetic collision cross-section, and other experimental
                 data by Bondi and later workers. The uncertainty in these values is on the order of 0.1 Å.

src/pymatgen/core/units.py

@@ -534,7 +534,7 @@ def __new__(
         return obj
 
     def __array_finalize__(self, obj) -> None:
-        """See http://docs.scipy.org/doc/numpy/user/basics.subclassing.html
+        """See https://docs.scipy.org/doc/numpy/user/basics.subclassing.html
         for comments.
         """
         if obj is None:

src/pymatgen/core/xcfunc.py

@@ -102,7 +102,7 @@ class type_name(NamedTuple):
     }
 
     # Correspondence between Abinit ixc notation and libxc notation.
-    # see: http://www.abinit.org/doc/helpfiles/for-v7.8/input_variables/varbas.html#ixc
+    # see: https://docs.abinit.org/variables/basic/#ixc
     # and 42_libpaw/m_pawpsp.F90 for the implementation.
     # Fortunately, all the other cases are handled with libxc.
     abinitixc_to_libxc: ClassVar[dict[int, dict[str, LibxcFunc]]] = {

src/pymatgen/electronic_structure/plotter.py

@@ -2238,7 +2238,7 @@ def _make_ticks_selected(self, ax: plt.Axes, branches: list[int]) -> tuple[plt.A
 class BSDOSPlotter:
     """A joint, aligned band structure and density of states plot. Contributions
     from Jan Pohls as well as the online example from Germain Salvato-Vallverdu:
-    http://gvallver.perso.univ-pau.fr/?p=587.
+    https://gvallver.perso.univ-pau.fr/?p=587.
     """
 
     def __init__(

src/pymatgen/ext/cod.py

@@ -90,7 +90,7 @@ def get_structure_by_id(self, cod_id: int, timeout: int = 600, **kwargs) -> Stru
         Returns:
             A Structure.
         """
-        response = requests.get(f"http://{self.url}/cod/{cod_id}.cif", timeout=timeout)
+        response = requests.get(f"https://{self.url}/cod/{cod_id}.cif", timeout=timeout)
         return Structure.from_str(response.text, fmt="cif", **kwargs)
 
     @requires(which("mysql"), "mysql must be installed to use this query.")
@@ -112,7 +112,7 @@ def get_structure_by_formula(self, formula: str, **kwargs) -> list[dict[str, str
         for line in text:
             if line.strip():
                 cod_id, sg = line.split("\t")
-                response = requests.get(f"http://www.crystallography.net/cod/{cod_id.strip()}.cif", timeout=600)
+                response = requests.get(f"https://{self.url}/cod/{cod_id.strip()}.cif", timeout=600)
                 try:
                     struct = Structure.from_str(response.text, fmt="cif", **kwargs)
                     structures.append({"structure": struct, "cod_id": int(cod_id), "sg": sg})

src/pymatgen/ext/optimade.py

@@ -59,7 +59,7 @@ class OptimadeRester:
     # regenerate on-demand from official providers.json using OptimadeRester.refresh_aliases()
     # these aliases are provided as a convenient shortcut for users of the OptimadeRester class
     aliases: ClassVar[dict[str, str]] = {
-        "aflow": "http://aflow.org/API/optimade/",
+        "aflow": "https://aflow.org/API/optimade/",
         "alexandria": "https://alexandria.icams.rub.de/pbe",
         "alexandria.pbe": "https://alexandria.icams.rub.de/pbe",
         "alexandria.pbesol": "https://alexandria.icams.rub.de/pbesol",
@@ -82,8 +82,8 @@ class OptimadeRester:
         "odbx": "https://optimade.odbx.science",
         "odbx.odbx_misc": "https://optimade-misc.odbx.science",
         "odbx.gnome": "https://optimade-gnome.odbx.science",
-        "omdb.omdb_production": "http://optimade.openmaterialsdb.se",
-        "oqmd": "http://oqmd.org/optimade/",
+        "omdb.omdb_production": "https://optimade.openmaterialsdb.se",
+        "oqmd": "https://oqmd.org/optimade/",
         "jarvis": "https://jarvis.nist.gov/optimade/jarvisdft",
         "tcod": "https://www.crystallography.net/tcod/optimade",
         "twodmatpedia": "http://optimade.2dmatpedia.org",

src/pymatgen/io/abinit/abiobjects.py

@@ -56,7 +56,7 @@ def lattice_from_abivars(cls=None, *args, **kwargs):
             raise ValueError(f"The sum of angdeg must be lower than 360, {ang_deg=}")
 
         # This code follows the implementation in ingeo.F90
-        # See also http://www.abinit.org/doc/helpfiles/for-v7.8/input_variables/varbas.html#angdeg
+        # See also https://docs.abinit.org/variables/basic/#angdeg
         tol12 = 1e-12
         pi, sin, cos, sqrt = np.pi, np.sin, np.cos, np.sqrt
         r_prim = np.zeros((3, 3))

src/pymatgen/io/abinit/netcdf.py

@@ -73,7 +73,7 @@ class NetcdfReader:
     Wraps and extends netCDF4.Dataset. Read only mode. Supports with statements.
 
     Additional documentation available at:
-        http://netcdf4-python.googlecode.com/svn/trunk/docs/netCDF4-module.html
+        https://unidata.github.io/netcdf4-python/
     """
 
     Error = NetcdfReaderError

src/pymatgen/io/babel.py

@@ -36,7 +36,7 @@
 needs_openbabel = requires(
     openbabel,
     "BabelMolAdaptor requires openbabel to be installed with Python bindings. "
-    "Please get it at http://openbabel.org (version >=3.0.0).",
+    "Please get it at https://openbabel.org (version >=3.0.0).",
 )
 
 

src/pymatgen/io/exciting/inputs.py

@@ -197,7 +197,7 @@ def write_etree(self, celltype, cartesian=False, bandstr=False, symprec: float =
         """
         root = ET.Element("input")
         root.set(
-            "{http://www.w3.org/2001/XMLSchema-instance}noNamespaceSchemaLocation",
+            "{https://www.w3.org/2001/XMLSchema-instance}noNamespaceSchemaLocation",
             "http://xml.exciting-code.org/excitinginput.xsd",
         )
         title = ET.SubElement(root, "title")

src/pymatgen/io/packmol.py

@@ -6,7 +6,7 @@
 which returns a PackmolSet object.
 
 For the run() method to work, you need to install the PACKMOL package.
-See http://m3g.iqm.unicamp.br/packmol for download and setup instructions.
+See https://m3g.iqm.unicamp.br/packmol for download and setup instructions.
 After installation, you may need to add the path of the PACKMOL
 executable to the PATH environment variable.
 

src/pymatgen/io/prismatic.py

@@ -1,4 +1,4 @@
-"""Write Prismatic (http://prism-em.com) input files."""
+"""Write Prismatic (https://prism-em.com) input files."""
 
 from __future__ import annotations
 
@@ -9,7 +9,7 @@
 
 
 class Prismatic:
-    """Write Prismatic  (http://prism-em.com) input files.
+    """Write Prismatic (https://prism-em.com) input files.
     This is designed for STEM image simulation.
     """
 

src/pymatgen/io/vasp/help.py

@@ -19,7 +19,7 @@ class VaspDoc:
     @requires(BeautifulSoup, "BeautifulSoup must be installed to fetch from the VASP wiki.")
     def __init__(self) -> None:
         """Init for VaspDoc."""
-        self.url_template = "http://www.vasp.at/wiki/index.php/%s"
+        self.url_template = "https://www.vasp.at/wiki/index.php/%s"
 
     def print_help(self, tag: str) -> None:
         """

src/pymatgen/io/vasp/sets.py

@@ -1986,7 +1986,7 @@ def kpoints_updates(self) -> dict[str, Any]:
 class MVLElasticSet(VaspInputSet):
     """
     MVL denotes VASP input sets that are implemented by the Materials Virtual
-    Lab (http://materialsvirtuallab.org) for various research.
+    Lab (https://materialsvirtuallab.org) for various research.
 
     This input set is used to calculate elastic constants in VASP. It is used
     in the following work::
@@ -2019,7 +2019,7 @@ def incar_updates(self) -> dict[str, Any]:
 class MVLGWSet(VaspInputSet):
     """
     MVL denotes VASP input sets that are implemented by the Materials Virtual
-    Lab (http://materialsvirtuallab.org) for various research. This is a
+    Lab (https://materialsvirtuallab.org) for various research. This is a
     flexible input set for GW calculations.
 
     Note that unlike all other input sets in this module, the PBE_54 series of

src/pymatgen/io/zeopp.py

@@ -9,8 +9,8 @@
 
 Zeo++ Installation Steps:
 ========================
-A stable version of Zeo++ can be obtained from http://zeoplusplus.org.
-Instructions can be found at http://www.zeoplusplus.org/download.html
+A stable version of Zeo++ can be obtained from https://zeoplusplus.org.
+Instructions can be found at https://www.zeoplusplus.org/download.html
 
 Zeo++ Post-Installation Checking:
 ==============================

src/pymatgen/phonon/bandstructure.py

@@ -507,14 +507,14 @@ def get_branch(self, index: int) -> list[dict[str, str | int]]:
 
     def write_phononwebsite(self, filename: str | PathLike) -> None:
         """Write a JSON file for the phononwebsite:
-        http://henriquemiranda.github.io/phononwebsite.
+        https://henriquemiranda.github.io/phononwebsite.
         """
         with open(filename, mode="w") as file:
             json.dump(self.as_phononwebsite(), file)
 
     def as_phononwebsite(self) -> dict:
         """Return a dictionary with the phononwebsite format:
-        http://henriquemiranda.github.io/phononwebsite.
+        https://henriquemiranda.github.io/phononwebsite.
         """
         assert self.structure is not None, "Structure is required for as_phononwebsite"
         dct = {}

src/pymatgen/symmetry/analyzer.py

@@ -1,5 +1,5 @@
 """An interface to the excellent spglib library by Atsushi Togo
-(http://spglib.sourceforge.net/) for pymatgen.
+(https://github.com/spglib/spglib) for pymatgen.
 
 v1.0 - Now works with both ordered and disordered structure.
 v2.0 - Updated for spglib 1.6.

src/pymatgen/util/coord.py

@@ -348,7 +348,7 @@ def get_angle(v1: ArrayLike, v2: ArrayLike, units: Literal["degrees", "radians"]
 
 
 class Simplex(MSONable):
-    """A generalized simplex object. See http://wikipedia.org/wiki/Simplex.
+    """A generalized simplex object. See https://wikipedia.org/wiki/Simplex.
 
     Attributes:
         space_dim (int): Dimension of the space. Usually, this is 1 more than the simplex_dim.

src/pymatgen/util/graph_hashing.py

@@ -117,7 +117,7 @@ def weisfeiler_lehman_graph_hash(graph: nx.Graph, edge_attr=None, node_attr=None
         .. [1] Shervashidze, Nino, Pascal Schweitzer, Erik Jan Van Leeuwen,
         Kurt Mehlhorn, and Karsten M. Borgwardt. Weisfeiler Lehman
         Graph Kernels. Journal of Machine Learning Research. 2011.
-        http://www.jmlr.org/papers/volume12/shervashidze11a/shervashidze11a.pdf
+        https://www.jmlr.org/papers/volume12/shervashidze11a/shervashidze11a.pdf
 
     See Also:
         weisfeiler_lehman_subgraph_hashes
@@ -216,7 +216,7 @@ def weisfeiler_lehman_subgraph_hashes(graph, edge_attr=None, node_attr=None, ite
         .. [1] Shervashidze, Nino, Pascal Schweitzer, Erik Jan Van Leeuwen,
         Kurt Mehlhorn, and Karsten M. Borgwardt. Weisfeiler Lehman
         Graph Kernels. Journal of Machine Learning Research. 2011.
-        http://www.jmlr.org/papers/volume12/shervashidze11a/shervashidze11a.pdf
+        https://www.jmlr.org/papers/volume12/shervashidze11a/shervashidze11a.pdf
         .. [2] Annamalai Narayanan, Mahinthan Chandramohan, Rajasekar Venkatesan,
         Lihui Chen, Yang Liu and Shantanu Jaiswa. graph2vec: Learning
         Distributed Representations of Graphs. arXiv. 2017

tests/ext/test_matproj.py

@@ -81,7 +81,7 @@ def test_get_data(self):
             "total_magnetization",
         }
         mp_id = "mp-1143"
-        vals = requests.get(f"http://legacy.materialsproject.org/materials/{mp_id}/json/", timeout=600)
+        vals = requests.get(f"https://legacy.materialsproject.org/materials/{mp_id}/json/", timeout=600)
         expected_vals = vals.json()
 
         for prop in props:
@@ -575,7 +575,7 @@ def test_get_all_materials_ids_doc(self):
     #         "total_magnetization",
     #     }
     #     mp_id = "mp-1143"
-    #     vals = requests.get(f"http://legacy.materialsproject.org/materials/{mp_id}/json/", timeout=600)
+    #     vals = requests.get(f"https://legacy.materialsproject.org/materials/{mp_id}/json/", timeout=600)
     #     expected_vals = vals.json()
     #
     #     for prop in props:

tests/files/io/exciting/input_exciting2.xml

@@ -1,4 +1,4 @@
-<input xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://xml.exciting-code.org/excitinginput.xsd">
+<input xmlns:ns0="https://www.w3.org/2001/XMLSchema-instance" ns0:noNamespaceSchemaLocation="http://xml.exciting-code.org/excitinginput.xsd">
   <title>Si2</title>
   <structure speciespath="./">
     <crystal scale="1.8897543760313331">

tests/io/exciting/test_inputs.py

@@ -35,8 +35,8 @@ def test_fromfile(self):
     def test_write_string(self):
         # Test for the string export of structure into the exciting input xml schema
         input_string = (
-            '<input xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" '
-            'xsi:noNamespaceSchemaLocation="http://xml.exciting-code.org/excitinginput'
+            '<input xmlns:ns0="https://www.w3.org/2001/XMLSchema-instance" '
+            'ns0:noNamespaceSchemaLocation="http://xml.exciting-code.org/excitinginput'
             '.xsd">\n  <title>Na4 Cl4</title>\n  <structure speciespath="./">\n    '
             '<crystal scale="1.8897543768634038">\n      <basevect>      5.62000000'
             "       0.00000000       0.00000000</basevect>\n      <basevect>      "

tests/symmetry/test_settings.py

@@ -78,7 +78,7 @@ def test_transform_coords(self):
 
     def test_transform_symmops(self):
         # reference data for this test taken from GENPOS
-        # http://cryst.ehu.es/cryst/get_gen.html
+        # https://cryst.ehu.es/cryst/get_gen.html
 
         # Fm-3m
         input_symm_ops = """x,y,z

tests/util/test_provenance.py

@@ -27,7 +27,9 @@ def setUp(self):
         self.s2 = Structure(np.eye(3, 3) * 3, ["Al"], [[0, 0, 0]])
         self.mol = Molecule(["He"], [[0, 0, 0]])
         # set up BibTeX strings
-        self.matproj = "@misc{MaterialsProject,\ntitle = {{Materials Project}},\nurl = {http://materialsproject.org}\n}"
+        self.matproj = (
+            "@misc{MaterialsProject,\ntitle = {{Materials Project}},\nurl = {https://materialsproject.org}\n}"
+        )
         self.pmg = (
             "@article{Ong2013,\n author = {Ong, "
             "Shyue Ping and Richards, William Davidson and Jain, "