Migrate to new MP API, fix failing examples

.github/workflows/test.yml

@@ -1,5 +1,4 @@
-# Runs the complete test suite incl. many external command line dependencies (like Openbabel)
-# as well as the pymatgen.ext package. Coverage used to be computed based on this workflow.
+# Runs the complete test suite incl. many external dependencies (like Openbabel)
 name: Tests
 
 on:
@@ -19,40 +18,44 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        # pytest-split automatically distributes work load so parallel jobs finish in similar time
         os: [ubuntu-latest]
         python-version: ["3.11"]
 
     runs-on: ${{ matrix.os }}
 
     env:
       PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
-      PMG_VASP_PSP_DIR: /home/runner/work/matgenb/matgenb/psp
+      PMG_VASP_PSP_DIR: "${{ github.workspace }}/psp"
+      MPLBACKEND: Agg  # non-interactive backend for matplotlib
 
     steps:
       - name: Check out repo
         uses: actions/checkout@v4
 
       - name: Set up micromamba
         uses: mamba-org/setup-micromamba@main
-
-      - name: Create mamba environment
-        run: |
-          micromamba create -n venv python=${{ matrix.python-version }} --yes
-          micromamba install -n venv -c conda-forge enumlib packmol bader openbabel openff-toolkit --yes
+        with:
+          environment-name: matgenb
+          condarc: |
+            channels:
+              - conda-forge
+          create-args: >-
+            python=${{ matrix.python-version }}
+            enumlib
+            packmol
+            bader
+            openbabel
+            openff-toolkit
 
       - name: Install uv
-        run: micromamba run -n venv pip install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          version: "latest"
 
       - name: Install dependencies
         run: |
-          micromamba activate venv
-          uv pip install numpy cython
-          uv pip install --upgrade -r requirements-ci.txt
+          micromamba run -n matgenb uv pip install --upgrade -r requirements-ci.txt
 
-      - name: pytest
+      - name: Run pytest
         run: |
-          micromamba activate venv
-          cd notebooks
-          pwd
-          pytest --ignore-glob=*notest.ipynb --nbmake .
+          micromamba run -n matgenb pytest --ignore-glob=*notest.ipynb --nbmake notebooks/

.pre-commit-config.yaml

@@ -5,48 +5,43 @@ ci:
 
 repos:
   - repo: https://github.com/psf/black
-    rev: 22.10.0
+    rev: 24.10.0
     hooks:
       - id: black-jupyter
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
+    rev: 7.1.1
     hooks:
       - id: flake8
         additional_dependencies: [flake8-bugbear]
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.2.3
+    rev: v3.19.0
     hooks:
       - id: pyupgrade
         args: [--py39-plus]
 
   - repo: https://github.com/PyCQA/autoflake
-    rev: v2.0.0
+    rev: v2.3.1
     hooks:
       - id: autoflake
 
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.991
-    hooks:
-      - id: mypy
-
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.5.3
+    rev: 1.9.1
     hooks:
       - id: nbqa-pyupgrade
         args: [--py39-plus]
       - id: nbqa-isort
 
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.1
+    rev: 0.8.1
     hooks:
       - id: nbstripout
         args: [--drop-empty-cells, --keep-output]

README.md

@@ -80,7 +80,7 @@ anyone is welcome to contribute.
 
    ```sh
    # Uncomment the subsequent lines in this cell to install dependencies for Google Colab.
-   # !pip install pymatgen==2022.2.27
+   # !pip install -U pymatgen
    ```
 
 4. Ideally, please update notebooks as needed to use more modern versions of the codes, and you may update the date of

docs/index.md

@@ -2,12 +2,12 @@ Visit the [Github Pages](http://matgenb.materialsvirtuallab.org) for a nicely fo
 
 # Introduction
 
-This repo is started by the [Materials Virtual Lab](http://www.materialsvirtuallab.org) as a useful collection of 
+This repo is started by the [Materials Virtual Lab](http://www.materialsvirtuallab.org) as a useful collection of
 Jupyter notebooks that demonstrate the utilization of open-source codes for the study of materials science.
 
 We frequently get requests (from students, postdocs, collaborators, or just general users) for example codes that
 demonstrate various capabilities in the open-source software we maintain and contribute to, such as the Materials
-Project software stack comprising [Python Materials Genomics (pymatgen)](http://www.pymatgen.org), 
+Project software stack comprising [Python Materials Genomics (pymatgen)](http://www.pymatgen.org),
 [Custodian](https://materialsprojecthub.io/custodian/), and [Fireworks](https://pythonhosted.org/FireWorks/). This
 repo is a start at building a more sustainable path towards sharing of code examples.
 
@@ -18,7 +18,7 @@ anyone is welcome to contribute.
 
 ## Option 1: Google Colab
 
-You can easily run all the notebooks via [Google Colab](https://colab.research.google.com/). 
+You can easily run all the notebooks via [Google Colab](https://colab.research.google.com/).
 
 ## Option 2: BinderHub
 
@@ -46,13 +46,13 @@ output.
 
 3. Notebooks should be well-documented and simple. The idea here is to be pedagogical. A newcomer to the software
    (with the right materials science background) should be able to follow the logic without too much difficulty. Feel
-   free to add authorship and contact information, as well as works to cite and acknowledge your contributions. In view 
+   free to add authorship and contact information, as well as works to cite and acknowledge your contributions. In view
    that scientific codes tend to be continuously being updated, please put in a list of the key pinned dependencies so
    that other users can install the exact version of software to run the notebook if needed. The best practice is to put
    a section that provides a commented out pip install instructure that can be used in Google Colab. For example,
    ```sh
    # Uncomment the subsequent lines in this cell to install dependencies for Google Colab.
-   # !pip install pymatgen==2022.2.27
+   # !pip install -U pymatgen
    ```
 
 4. Ideally, please update notebooks as needed to use more modern versions of the codes, and you may update the date of

notebooks/2013-01-01-Calculating Reaction Energies with the Materials API.ipynb

@@ -14,7 +14,7 @@
    "outputs": [],
    "source": [
     "# Uncomment the subsequent lines in this cell to install dependencies for Google Colab.\n",
-    "# !pip install pymatgen==2022.7.19"
+    "# !pip install -U pymatgen"
    ]
   },
   {
@@ -47,18 +47,18 @@
     }
    ],
    "source": [
+    "from mp_api.client import MPRester\n",
     "from pymatgen.analysis.reaction_calculator import ComputedReaction\n",
     "from pymatgen.core import Composition\n",
     "from pymatgen.core.units import FloatWithUnit\n",
-    "from pymatgen.entries.computed_entries import ComputedEntry\n",
-    "from pymatgen.ext.matproj import MPRester\n",
     "\n",
     "# This initializes the REST adaptor. Put your own API key in if necessary.\n",
     "mpr = MPRester()\n",
     "\n",
     "# This gets all entries belonging to the Ca-C-O system.\n",
     "all_entries = mpr.get_entries_in_chemsys([\"Ca\", \"C\", \"O\"])\n",
     "\n",
+    "\n",
     "# This method simply gets the lowest energy entry for all entry with the same composition.\n",
     "def get_most_stable_entry(formula):\n",
     "    relevant_entries = [\n",

notebooks/2013-01-01-Calculating XRD patterns.ipynb

@@ -16,7 +16,7 @@
    "outputs": [],
    "source": [
     "# Uncomment the subsequent lines in this cell to install dependencies for Google Colab.\n",
-    "# !pip install pymatgen==2022.2.27"
+    "# !pip install -U pymatgen"
    ]
   },
   {

notebooks/2013-01-01-Getting crystal structures from online sources.ipynb

@@ -16,8 +16,7 @@
    "outputs": [],
    "source": [
     "# Uncomment the subsequent lines in this cell to install dependencies for Google Colab.\n",
-    "# !pip install pymatgen==2022.7.19\n",
-    "from __future__ import annotations"
+    "# !pip install -U pymatgen"
    ]
   },
   {
@@ -35,7 +34,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pymatgen.ext.matproj import MPRester\n",
+    "from mp_api.client import MPRester\n",
     "\n",
     "# Note that you will need to add your Materials API key in your .pmgrc.yaml file as \"PMG_MAPI_KEY\".\n",
     "# Alternatively, you will need to supply the API key as an arg to MPRester.\n",

notebooks/2013-01-01-Molecule.ipynb

@@ -21,8 +21,7 @@
    "outputs": [],
    "source": [
     "# Uncomment the subsequent lines in this cell to install dependencies for Google Colab.\n",
-    "# !pip install pymatgen==2022.7.19\n",
-    "from __future__ import annotations"
+    "# !pip install -U pymatgen"
    ]
   },
   {

notebooks/2013-01-01-Ordering Disordered Structures.ipynb

@@ -16,7 +16,7 @@
    "outputs": [],
    "source": [
     "# Uncomment the subsequent lines in this cell to install dependencies for Google Colab.\n",
-    "# !pip install pymatgen==2022.7.19"
+    "# !pip install -U pymatgen"
    ]
   },
   {

notebooks/2013-01-01-Plotting and Analyzing a Phase Diagram using the Materials API.ipynb

@@ -16,8 +16,7 @@
    "outputs": [],
    "source": [
     "# Uncomment the subsequent lines in this cell to install dependencies for Google Colab.\n",
-    "# !pip install pymatgen==2022.7.19\n",
-    "from __future__ import annotations"
+    "# !pip install -U pymatgen"
    ]
   },
   {
@@ -26,8 +25,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "from mp_api.client import MPRester\n",
     "from pymatgen.analysis.phase_diagram import PDPlotter, PhaseDiagram\n",
-    "from pymatgen.ext.matproj import MPRester\n",
     "\n",
     "%matplotlib inline"
    ]

notebooks/2013-01-01-Plotting the electronic structure of Fe.ipynb

@@ -14,8 +14,7 @@
    "outputs": [],
    "source": [
     "# Uncomment the subsequent lines in this cell to install dependencies for Google Colab.\n",
-    "# !pip install pymatgen==2022.7.19\n",
-    "from __future__ import annotations"
+    "# !pip install -U pymatgen"
    ]
   },
   {

notebooks/2013-01-01-Units.ipynb

@@ -28,8 +28,7 @@
    "outputs": [],
    "source": [
     "# Uncomment the subsequent lines in this cell to install dependencies for Google Colab.\n",
-    "# !pip install pymatgen==2022.7.19\n",
-    "from __future__ import annotations"
+    "# !pip install -U pymatgen"
    ]
   },
   {

notebooks/2016-09-08-Data-driven First Principles Methods for the Study and Design of Alkali Superionic Conductors Part 1 - Structure Generation.ipynb

@@ -23,8 +23,7 @@
    "outputs": [],
    "source": [
     "# Uncomment the subsequent lines in this cell to install dependencies for Google Colab.\n",
-    "# !pip install pymatgen==2022.7.19\n",
-    "from __future__ import annotations"
+    "# !pip install -U pymatgen"
    ]
   },
   {

notebooks/2016-09-08-Data-driven First Principles Methods for the Study and Design of Alkali Superionic Conductors Part 2 - Phase and Electrochemical Stability.ipynb

@@ -23,8 +23,7 @@
    "outputs": [],
    "source": [
     "# Uncomment the subsequent lines in this cell to install dependencies for Google Colab.\n",
-    "# !pip install pymatgen==2022.7.19 pymatgen-analysis-diffusion\n",
-    "from __future__ import annotations"
+    "# !pip install -U pymatgen pymatgen-analysis-diffusion"
    ]
   },
   {
@@ -40,6 +39,7 @@
     "\n",
     "import matplotlib as mpl\n",
     "import palettable\n",
+    "from mp_api.client import MPRester\n",
     "from pymatgen.analysis.phase_diagram import (\n",
     "    CompoundPhaseDiagram,\n",
     "    PDPlotter,\n",
@@ -48,7 +48,6 @@
     "from pymatgen.core import Composition, Element\n",
     "from pymatgen.entries.compatibility import MaterialsProjectCompatibility\n",
     "from pymatgen.entries.computed_entries import ComputedEntry\n",
-    "from pymatgen.ext.matproj import MPRester\n",
     "from pymatgen.io.vasp import Vasprun\n",
     "from pymatgen.util.plotting import pretty_plot"
    ]

notebooks/2016-09-08-Data-driven First Principles Methods for the Study and Design of Alkali Superionic Conductors Part 3 - Diffusivity and Ionic Conductivity.ipynb

@@ -23,8 +23,7 @@
    "outputs": [],
    "source": [
     "# Uncomment the subsequent lines in this cell to install dependencies for Google Colab.\n",
-    "# !pip install pymatgen==2022.7.19 pymatgen-analysis-diffusion\n",
-    "from __future__ import annotations"
+    "# !pip install -U pymatgen pymatgen-analysis-diffusion"
    ]
   },
   {

notebooks/2016-09-25-Plotting phonon bandstructure and dos.ipynb

@@ -16,8 +16,7 @@
    "outputs": [],
    "source": [
     "# Uncomment the subsequent lines in this cell to install dependencies for Google Colab.\n",
-    "# !pip install pymatgen==2022.7.19 phonopy\n",
-    "from __future__ import annotations"
+    "# !pip install -U pymatgen phonopy"
    ]
   },
   {

notebooks/2017-03-02-Getting data from Materials Project.ipynb

@@ -16,7 +16,7 @@
    "outputs": [],
    "source": [
     "# Uncomment the subsequent lines in this cell to install dependencies for Google Colab.\n",
-    "# !pip install pymatgen==2022.7.19"
+    "# !pip install -U pymatgen"
    ]
   },
   {
@@ -26,10 +26,9 @@
    "outputs": [],
    "source": [
     "import pprint\n",
-    "import re\n",
     "\n",
+    "from mp_api.client import MPRester\n",
     "from pymatgen.core import Composition\n",
-    "from pymatgen.ext.matproj import MPRester\n",
     "\n",
     "# Make sure that you have the Materials API key. Put the key in the call to\n",
     "# MPRester if needed, e.g, MPRester(\"MY_API_KEY\")\n",

notebooks/2017-04-03-Slab generation and Wulff shape.ipynb

@@ -27,7 +27,7 @@
    "outputs": [],
    "source": [
     "# Uncomment the subsequent lines in this cell to install dependencies for Google Colab.\n",
-    "# !pip install pymatgen==2022.7.19"
+    "# !pip install -U pymatgen"
    ]
   },
   {
@@ -37,7 +37,7 @@
    "outputs": [],
    "source": [
     "# Import the necessary tools for making a Wulff shape\n",
-    "from __future__ import annotations\n",
+    "\n",
     "\n",
     "from pymatgen.analysis.wulff import WulffShape\n",
     "\n",

notebooks/2017-04-14-Inputs and Analysis of VASP runs.ipynb

@@ -16,7 +16,7 @@
    "outputs": [],
    "source": [
     "# Uncomment the subsequent lines in this cell to install dependencies for Google Colab.\n",
-    "# !pip install pymatgen==2022.7.19"
+    "# !pip install -U pymatgen"
    ]
   },
   {