Merge branch 'develop' into fixing-step-function

.all-contributorsrc

@@ -836,6 +836,16 @@
       "contributions": [
         "code"
       ]
+    },
+    {
+      "login": "lorenzofavaro",
+      "name": "Lorenzo",
+      "avatar_url": "https://avatars.githubusercontent.com/u/44714920?v=4",
+      "profile": "https://github.com/lorenzofavaro",
+      "contributions": [
+        "code",
+        "test"
+      ]
     }
   ],
   "contributorsPerLine": 7,

CHANGELOG.md

@@ -23,6 +23,7 @@
 
 ## Breaking changes
 
+- Integrated the `[pandas]` extra into the core PyBaMM package, deprecating the `pybamm[pandas]` optional dependency. Pandas is now a required dependency and will be installed upon installing PyBaMM ([#3892](https://github.com/pybamm-team/PyBaMM/pull/3892))
 - Renamed "have_optional_dependency" to "import_optional_dependency" ([#3866](https://github.com/pybamm-team/PyBaMM/pull/3866))
 - Integrated the `[latexify]` extra into the core PyBaMM package, deprecating the `pybamm[latexify]` set of optional dependencies. SymPy is now a required dependency and will be installed upon installing PyBaMM ([#3848](https://github.com/pybamm-team/PyBaMM/pull/3848))
 - Renamed "testing" argument for plots to "show_plot" and flipped its meaning (show_plot=True is now the default and shows the plot) ([#3842](https://github.com/pybamm-team/PyBaMM/pull/3842))

all_contributors.md

@@ -104,6 +104,9 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
       <td align="center" valign="top" width="14.28%"><a href="http://akhilsharma.info"><img src="https://avatars.githubusercontent.com/u/68015525?v=4?s=100" width="100px;" alt="AKHIL SHARMA"/><br /><sub><b>AKHIL SHARMA</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=Akhil-Sharma30" title="Documentation">📖</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/HarshvirSandhu"><img src="https://avatars.githubusercontent.com/u/75773763?v=4?s=100" width="100px;" alt="Harshvir Sandhu"/><br /><sub><b>Harshvir Sandhu</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=HarshvirSandhu" title="Code">💻</a></td>
     </tr>
+    <tr>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/lorenzofavaro"><img src="https://avatars.githubusercontent.com/u/44714920?v=4?s=100" width="100px;" alt="Lorenzo"/><br /><sub><b>Lorenzo</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=lorenzofavaro" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=lorenzofavaro" title="Tests">⚠️</a></td>
+    </tr>
   </tbody>
 </table>
 

docs/source/user_guide/installation/index.rst

@@ -69,6 +69,7 @@ Package                                                             Minimum supp
 `Anytree <https://anytree.readthedocs.io/en/stable/>`__             2.8.0
 `SymPy <https://docs.sympy.org/latest/index.html>`__                1.9.3
 `typing-extensions <https://pypi.org/project/typing-extensions/>`__ 4.10.0
+`pandas <https://pypi.org/project/pandas/>`__                       1.5.0
 =================================================================== ==========================
 
 .. _install.optional_dependencies:
@@ -97,19 +98,6 @@ Dependency                                                  Minimum Version    p
 `matplotlib <https://matplotlib.org/stable/>`__             3.6.0              plot               To plot various battery models, and analyzing battery performance.
 =========================================================== ================== ================== ==================================================================
 
-.. _install.pandas_dependencies:
-
-Pandas dependencies
-^^^^^^^^^^^^^^^^^^^
-
-Installable with ``pip install "pybamm[pandas]"``
-
-=========================================================== ================== ================== ==================================================================
-Dependency                                                  Minimum Version    pip extra          Notes
-=========================================================== ================== ================== ==================================================================
-`pandas <https://pandas.pydata.org/docs/>`__                1.5.0              pandas             For data manipulation and analysis.
-=========================================================== ================== ================== ==================================================================
-
 .. _install.docs_dependencies:
 
 Docs dependencies

pyproject.toml

@@ -43,6 +43,7 @@ dependencies = [
     "anytree>=2.8.0",
     "sympy>=1.12",
     "typing-extensions>=4.10.0",
+    "pandas>=1.5.0"
 ]
 
 [project.urls]
@@ -112,10 +113,8 @@ dev = [
     "pytest>=6",
     "pytest-xdist",
     "nbmake",
-]
-# Reading CSV files
-pandas = [
-    "pandas>=1.5.0",
+    # To access the metadata for python packages
+    "importlib-metadata; python_version < '3.10'",
 ]
 # For the Jax solver. Note: these must be kept in sync with the versions defined in pybamm/util.py.
 jax = [
@@ -130,7 +129,7 @@ odes = [
 all = [
     "autograd>=1.6.2",
     "scikit-fem>=8.1.0",
-    "pybamm[examples,plot,cite,bpx,tqdm,pandas]",
+    "pybamm[examples,plot,cite,bpx,tqdm]",
 ]
 
 [project.scripts]

tests/__init__.py

@@ -37,5 +37,8 @@
     get_unit_2p1D_mesh_for_testing,
     get_cylindrical_discretisation_for_testing,
     get_base_model_with_battery_geometry,
+    get_required_distribution_deps,
+    get_optional_distribution_deps,
+    get_present_optional_import_deps,
 )
 from .testcase import TestCase

tests/shared.py

@@ -3,6 +3,13 @@
 #
 import pybamm
 from scipy.sparse import eye
+import sys
+import re
+
+if sys.version_info < (3, 10):
+    import importlib_metadata
+else:
+    import importlib.metadata as importlib_metadata
 
 
 class SpatialMethodForTesting(pybamm.SpatialMethod):
@@ -276,3 +283,35 @@ def get_base_model_with_battery_geometry(**kwargs):
     model = pybamm.BaseModel()
     model._geometry = pybamm.battery_geometry(**kwargs)
     return model
+
+
+def get_required_distribution_deps(package_name):
+    pattern = re.compile(r"(?!.*extra\b)^([^<>=;\[]+)\b.*$")
+    if json_deps := importlib_metadata.metadata(package_name).json.get("requires_dist"):
+        return {m.group(1) for dep_name in json_deps if (m := pattern.match(dep_name))}
+    return set()
+
+
+def get_optional_distribution_deps(package_name):
+    pattern = re.compile(rf"(?!.*{package_name}\b|.*docs\b|.*dev\b)^([^<>=;\[]+)\b.*$")
+    if json_deps := importlib_metadata.metadata(package_name).json.get("requires_dist"):
+        return {
+            m.group(1)
+            for dep_name in json_deps
+            if (m := pattern.match(dep_name)) and "extra" in m.group(0)
+        }
+    return set()
+
+
+def get_present_optional_import_deps(package_name, optional_distribution_deps=None):
+    if optional_distribution_deps is None:
+        optional_distribution_deps = get_optional_distribution_deps(package_name)
+
+    present_optional_import_deps = set()
+    for (
+        import_pkg,
+        distribution_pkgs,
+    ) in importlib_metadata.packages_distributions().items():
+        if any(dep in optional_distribution_deps for dep in distribution_pkgs):
+            present_optional_import_deps.add(import_pkg)
+    return present_optional_import_deps

tests/unit/test_util.py

@@ -1,6 +1,7 @@
 #
 # Tests the utility functions.
 #
+import importlib
 from tests import TestCase
 import numpy as np
 import os
@@ -10,9 +11,12 @@
 import unittest
 from unittest.mock import patch
 from io import StringIO
-from tempfile import TemporaryDirectory
 
-anytree = sys.modules["anytree"]
+from tests import (
+    get_optional_distribution_deps,
+    get_required_distribution_deps,
+    get_present_optional_import_deps,
+)
 
 
 class TestUtil(TestCase):
@@ -32,7 +36,6 @@ def test_rmse(self):
             pybamm.rmse(np.ones(5), np.zeros(3))
 
     def test_is_constant_and_can_evaluate(self):
-        sys.modules["anytree"] = anytree
         symbol = pybamm.PrimaryBroadcast(0, "negative electrode")
         self.assertEqual(False, pybamm.is_constant_and_can_evaluate(symbol))
         symbol = pybamm.StateVector(slice(0, 1))
@@ -100,27 +103,70 @@ def test_git_commit_info(self):
         self.assertEqual(git_commit_info[:2], "v2")
 
     def test_import_optional_dependency(self):
-        with self.assertRaisesRegex(
-            ModuleNotFoundError, "Optional dependency pybtex is not available."
-        ):
-            pybtex = sys.modules["pybtex"]
-            sys.modules["pybtex"] = None
-            pybamm.print_citations()
-        with self.assertRaisesRegex(
-            ModuleNotFoundError, "Optional dependency anytree is not available."
-        ):
-            with TemporaryDirectory() as dir_name:
-                sys.modules["anytree"] = None
-                test_stub = os.path.join(dir_name, "test_visualize")
-                test_name = f"{test_stub}.png"
-                c = pybamm.Variable("c", "negative electrode")
-                d = pybamm.Variable("d", "negative electrode")
-                sym = pybamm.div(c * pybamm.grad(c)) + (c / d + c - d) ** 5
-                sym.visualise(test_name)
-
-        sys.modules["pybtex"] = pybtex
-        pybamm.util.import_optional_dependency("pybtex")
-        pybamm.print_citations()
+        optional_distribution_deps = get_optional_distribution_deps("pybamm")
+        present_optional_import_deps = get_present_optional_import_deps(
+            "pybamm", optional_distribution_deps=optional_distribution_deps
+        )
+
+        # Save optional dependencies, then set to None
+        modules = {}
+        for import_pkg in present_optional_import_deps:
+            modules[import_pkg] = sys.modules.get(import_pkg)
+            sys.modules[import_pkg] = None
+
+        # Test import optional dependency
+        for import_pkg in present_optional_import_deps:
+            with self.assertRaisesRegex(
+                ModuleNotFoundError,
+                f"Optional dependency {import_pkg} is not available.",
+            ):
+                pybamm.util.import_optional_dependency(import_pkg)
+
+        # Restore optional dependencies
+        for import_pkg in present_optional_import_deps:
+            sys.modules[import_pkg] = modules[import_pkg]
+
+    def test_pybamm_import(self):
+        optional_distribution_deps = get_optional_distribution_deps("pybamm")
+        present_optional_import_deps = get_present_optional_import_deps(
+            "pybamm", optional_distribution_deps=optional_distribution_deps
+        )
+
+        # Save optional dependencies, then set to None
+        modules = {}
+        for import_pkg in present_optional_import_deps:
+            modules[import_pkg] = sys.modules.get(import_pkg)
+            sys.modules[import_pkg] = None
+
+        # Test pybamm is still importable
+        try:
+            importlib.reload(importlib.import_module("pybamm"))
+        except ModuleNotFoundError as error:
+            self.fail(
+                f"Import of 'pybamm' shouldn't require optional dependencies. Error: {error}"
+            )
+
+        # Restore optional dependencies
+        for import_pkg in present_optional_import_deps:
+            sys.modules[import_pkg] = modules[import_pkg]
+
+    def test_optional_dependencies(self):
+        optional_distribution_deps = get_optional_distribution_deps("pybamm")
+        required_distribution_deps = get_required_distribution_deps("pybamm")
+
+        # Get nested required dependencies
+        for distribution_dep in list(required_distribution_deps):
+            required_distribution_deps.update(
+                get_required_distribution_deps(distribution_dep)
+            )
+
+        # Check that optional dependencies are not present in the core PyBaMM installation
+        optional_present_deps = optional_distribution_deps & required_distribution_deps
+        self.assertFalse(
+            bool(optional_present_deps),
+            f"Optional dependencies installed: {optional_present_deps}.\n"
+            "Please ensure that optional dependencies are not present in the core PyBaMM installation, or list them as required.",
+        )
 
 
 class TestSearch(TestCase):