Sunset module pymatgen/util/serialization.py (#2736)

* remove all calls to pmg_serialize()

* rm pymatgen/util/serialization.py

* replace pymatgen.util.serialization.{pmg_pickle_dump, pmg_pickle_load} with regular pickle.dump/load

* remove serialization module from docs_rst

* typos

* format issue + PR templates

.github/ISSUE_TEMPLATE/bug_report.md

@@ -8,6 +8,7 @@ A clear and concise description of what the bug is.
 
 **To Reproduce**
 Steps to reproduce the behavior:
+
 1. Go to '...'
 2. Click on '....'
 3. Scroll down to '....'
@@ -24,8 +25,8 @@ If applicable, add screenshots to help explain your problem.
 
 **Desktop (please complete the following information):**
 
-- OS: [e.g. Mac,Windows,Linux]
-- Version [e.g. 2019.9.16]
+- OS: (e.g. Mac, Windows, Linux)
+- Version (e.g. 2022.11.17)
 
 **Additional context**
 Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -4,7 +4,7 @@ about: Suggest an idea for this project
 ---
 
 **Is your feature request related to a problem? Please describe.**
-A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+A clear and concise description of what the problem is. Ex. I'm always frustrated when (...)
 
 **Describe the solution you'd like**
 A clear and concise description of what you want to happen.

.github/PULL_REQUEST_TEMPLATE.md

@@ -7,25 +7,28 @@ Include a summary of major changes in bullet points:
 - Fix 1
 - Fix 2
 
-## TODO (if any)
+## Todo (if any)
 
-If this is a work-in-progress, write something about what else needs
-to be done
+If this is a work-in-progress, write something about what else needs to be done
 
 - Feature 1 supports A, but not B.
 
 ## Checklist
 
-Work-in-progress pull requests are encouraged, but please put [WIP]
-in the pull request title.
+Work-in-progress pull requests are encouraged, but please put \[WIP\] in the pull request title.
 
 Before a pull request can be merged, the following items must be checked:
 
-- [ ] Doc strings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
-      Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
-- [ ] Type annotations are **highly*- encouraged. Run [`mypy`](https://github.com/python/mypy) `path/to/file.py` to type check your code.
+- [ ] Doc strings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html). Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
+- [ ] Type annotations are *highly* encouraged. Run [`mypy path/to/file.py`](https://github.com/python/mypy) to type check your code.
 - [ ] Tests have been added for any new functionality or bug fixes.
 - [ ] All linting and tests pass.
 
-Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most
-errors prior to submitting the PR. We highly recommended installing `pre-commit` hooks. Simply `pip install -U pre-commit && pre-commit install` in the repo's root directory. Afterwards linters will run before every commit and abort if any issues pop up.
+Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most errors prior to submitting the PR. We highly recommended installing `pre-commit` hooks. Simply Run
+
+```sh
+pip install -U pre-commit
+pre-commit install
+```
+
+in the repo's root directory. Afterwards linters will run before every commit and abort if any issues pop up.

.github/dependabot.yml

@@ -1,6 +1,6 @@
 version: 2
 updates:
-  - package-ecosystem: "github-actions"
-    directory: "/"
+  - package-ecosystem: github-actions
+    directory: /
     schedule:
-      interval: "weekly"
+      interval: weekly

docs_rst/pymatgen.util.rst

@@ -23,7 +23,6 @@ Submodules
    pymatgen.util.num
    pymatgen.util.plotting
    pymatgen.util.provenance
-   pymatgen.util.serialization
    pymatgen.util.string
    pymatgen.util.testing
    pymatgen.util.typing

pymatgen/io/abinit/abiobjects.py

@@ -18,7 +18,6 @@
 from monty.json import MontyDecoder, MontyEncoder, MSONable
 
 from pymatgen.core import ArrayWithUnit, Lattice, Species, Structure, units
-from pymatgen.util.serialization import pmg_serialize
 
 
 def lattice_from_abivars(cls=None, *args, **kwargs):
@@ -388,10 +387,11 @@ def to_abivars(self):
             "nspden": self.nspden,
         }
 
-    @pmg_serialize
     def as_dict(self):
         """Convert object to dict."""
-        return {k: getattr(self, k) for k in self._fields}
+        out = {k: getattr(self, k) for k in self._fields}
+        out.update({"@module": type(self).__module__, "@class": type(self).__name__})
+        return out
 
     @classmethod
     def from_dict(cls, d):
@@ -499,10 +499,14 @@ def to_abivars(self):
             return {"occopt": 1, "tsmear": 0.0}
         return {"occopt": self.occopt, "tsmear": self.tsmear}
 
-    @pmg_serialize
     def as_dict(self):
         """json friendly dict representation of Smearing"""
-        return {"occopt": self.occopt, "tsmear": self.tsmear}
+        return {
+            "@module": type(self).__module__,
+            "@class": type(self).__name__,
+            "occopt": self.occopt,
+            "tsmear": self.tsmear,
+        }
 
     @staticmethod
     def from_dict(d):
@@ -539,10 +543,9 @@ def to_abivars(self):
         """Dictionary with Abinit input variables."""
         return self.copy()
 
-    @pmg_serialize
     def as_dict(self):
         """Convert object to dict."""
-        return self.copy()
+        return {"@module": type(self).__module__, "@class": type(self).__name__, **self.copy()}
 
     @classmethod
     def from_dict(cls, d):

pymatgen/io/abinit/inputs.py

@@ -22,7 +22,6 @@
 from pymatgen.io.abinit import abiobjects as aobj
 from pymatgen.io.abinit.pseudos import Pseudo, PseudoTable
 from pymatgen.io.abinit.variable import InputVariable
-from pymatgen.util.serialization import pmg_serialize
 
 logger = logging.getLogger(__file__)
 
@@ -769,7 +768,6 @@ def __init__(
         if comment is not None:
             self.set_comment(comment)
 
-    @pmg_serialize
     def as_dict(self):
         """
         JSON interface used in pymatgen for easier serialization.
@@ -781,12 +779,14 @@ def as_dict(self):
                 value = value.tolist()
             abi_args.append((key, value))
 
-        return dict(
-            structure=self.structure.as_dict(),
-            pseudos=[p.as_dict() for p in self.pseudos],
-            comment=self.comment,
-            abi_args=abi_args,
-        )
+        return {
+            "@module": type(self).__module__,
+            "@class": type(self).__name__,
+            "structure": self.structure.as_dict(),
+            "pseudos": [p.as_dict() for p in self.pseudos],
+            "comment": self.comment,
+            "abi_args": abi_args,
+        }
 
     @property
     def vars(self):

pymatgen/io/abinit/pseudos.py

@@ -26,7 +26,6 @@
 from pymatgen.core.periodic_table import Element
 from pymatgen.core.xcfunc import XcFunc
 from pymatgen.util.plotting import add_fig_kwargs, get_ax_fig_plt
-from pymatgen.util.serialization import pmg_serialize
 
 logger = logging.getLogger(__name__)
 
@@ -250,21 +249,22 @@ def supports_soc(self):
         Base classes should provide a concrete implementation that computes this value.
         """
 
-    @pmg_serialize
     def as_dict(self, **kwargs):
         """Return dictionary for MSONable protocol."""
         # pylint: disable=E1101
-        return dict(
-            basename=self.basename,
-            type=self.type,
-            symbol=self.symbol,
-            Z=self.Z,
-            Z_val=self.Z_val,
-            l_max=self.l_max,
-            md5=self.md5,
-            filepath=self.filepath,
-            # xc=self.xc.as_dict(),
-        )
+        return {
+            "@module": type(self).__module__,
+            "@class": type(self).__name__,
+            "basename": self.basename,
+            "type": self.type,
+            "symbol": self.symbol,
+            "Z": self.Z,
+            "Z_val": self.Z_val,
+            "l_max": self.l_max,
+            "md5": self.md5,
+            "filepath": self.filepath,
+            # "xc": self.xc.as_dict(),
+        }
 
     @classmethod
     def from_dict(cls, d):
@@ -596,10 +596,14 @@ def __str__(self):
             return f"ecut: {self.ecut}, pawecutdg: {self.pawecutdg}"
         return f"ecut: {self.ecut}"
 
-    @pmg_serialize
     def as_dict(self):
         """Return dictionary for MSONable protocol."""
-        return dict(ecut=self.ecut, pawecutdg=self.pawecutdg)
+        return {
+            "@module": type(self).__module__,
+            "@class": type(self).__name__,
+            "ecut": self.ecut,
+            "pawecutdg": self.pawecutdg,
+        }
 
     @classmethod
     def from_dict(cls, d):

pymatgen/util/convergence.py

@@ -11,10 +11,10 @@
 
 calculates which function fits best
 for tol < 0
-returns the x value for which y is converged within tol of the assymtotic value
+returns the x value for which y is converged within tol of the asymptotic value
 for tol > 0
 returns the x_value for which dy(x)/dx < tol for all x >= x_value, conv is true is such a x_value exists
-for the best fit a gnuplot line is printed plotting the data, the function and the assymthotic value
+for the best fit a gnuplot line is printed plotting the data, the function and the asymptotic value
 """
 
 import random
@@ -23,7 +23,6 @@
 import numpy as np
 
 __author__ = "Michiel van Setten"
-__copyright__ = " "
 __version__ = "0.9"
 __maintainer__ = "Michiel van Setten"
 __email__ = "mjvansetten@gmail.com"