From c135cf3a19023ccfb1847ca92621b9ba68069663 Mon Sep 17 00:00:00 2001
From: esoteric-ephemera <aaron.kaplan.physics@gmail.com>
Date: Thu, 22 Aug 2024 16:11:02 -0700
Subject: [PATCH 01/11] update spglib symmetry dataset access and pin min
 version

---
 matminer/featurizers/structure/bonding.py | 4 ++--
 pyproject.toml                            | 3 ++-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/matminer/featurizers/structure/bonding.py b/matminer/featurizers/structure/bonding.py
index f22a3cdbc..148fda9cc 100644
--- a/matminer/featurizers/structure/bonding.py
+++ b/matminer/featurizers/structure/bonding.py
@@ -805,8 +805,8 @@ def get_equiv_sites(self, s, site):
         sga = SpacegroupAnalyzer(s, symprec=0.01)
         sg = sga.get_space_group_operations
         sym_data = sga.get_symmetry_dataset()
-        equiv_atoms = sym_data["equivalent_atoms"]
-        wyckoffs = sym_data["wyckoffs"]
+        equiv_atoms = sym_data.equivalent_atoms
+        wyckoffs = sym_data.wyckoffs
         sym_struct = SymmetrizedStructure(s, sg, equiv_atoms, wyckoffs)
         equivs = sym_struct.find_equivalent_sites(site)
         return equivs
diff --git a/pyproject.toml b/pyproject.toml
index 71ec89d26..50f8d71bd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,7 +2,8 @@
 requires = [
      # pin NumPy version used in the build
      "numpy>=1.20.1",
-     "setuptools>=43.0.0"
+     "setuptools>=43.0.0",
+     "spglib>=2.5.0",
 ]
 build-backend = "setuptools.build_meta"
 

From c9bbaa991c8092f2f126e9936b29884b0a5e323e Mon Sep 17 00:00:00 2001
From: esoteric-ephemera <aaron.kaplan.physics@gmail.com>
Date: Fri, 23 Aug 2024 09:49:52 -0700
Subject: [PATCH 02/11] move spglib version pin

---
 pyproject.toml | 1 -
 setup.py       | 1 +
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 50f8d71bd..ce428dd9b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -3,7 +3,6 @@ requires = [
      # pin NumPy version used in the build
      "numpy>=1.20.1",
      "setuptools>=43.0.0",
-     "spglib>=2.5.0",
 ]
 build-backend = "setuptools.build_meta"
 
diff --git a/setup.py b/setup.py
index c0e79f2de..9f9ac8faf 100644
--- a/setup.py
+++ b/setup.py
@@ -63,6 +63,7 @@ def local_version(version):
             "sympy ~= 1.11",
             "monty >= 2023",
             "pymatgen >= 2023",
+            "spglib>=2.5.0",
         ],
         extras_require=extras_require,
         classifiers=[

From 9c6173678a039ae7b58d4356219119327b3e0a7a Mon Sep 17 00:00:00 2001
From: esoteric-ephemera <aaron.kaplan.physics@gmail.com>
Date: Fri, 23 Aug 2024 11:29:06 -0700
Subject: [PATCH 03/11] ensure correct spglib installed in requirements

---
 requirements/ubuntu-latest_py3.10.txt | 2 +-
 requirements/ubuntu-latest_py3.11.txt | 2 +-
 requirements/ubuntu-latest_py3.9.txt  | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/requirements/ubuntu-latest_py3.10.txt b/requirements/ubuntu-latest_py3.10.txt
index ab2cbb6cc..d01678499 100644
--- a/requirements/ubuntu-latest_py3.10.txt
+++ b/requirements/ubuntu-latest_py3.10.txt
@@ -266,7 +266,7 @@ soupsieve==2.5
     # via beautifulsoup4
 sparse==0.15.4
     # via dscribe
-spglib==2.4.0
+spglib==2.5.2
     # via pymatgen
 sphinx==7.3.7
     # via matminer (setup.py)
diff --git a/requirements/ubuntu-latest_py3.11.txt b/requirements/ubuntu-latest_py3.11.txt
index 7b8853fc1..209088fa1 100644
--- a/requirements/ubuntu-latest_py3.11.txt
+++ b/requirements/ubuntu-latest_py3.11.txt
@@ -264,7 +264,7 @@ soupsieve==2.5
     # via beautifulsoup4
 sparse==0.15.4
     # via dscribe
-spglib==2.4.0
+spglib==2.5.2
     # via pymatgen
 sphinx==7.3.7
     # via matminer (setup.py)
diff --git a/requirements/ubuntu-latest_py3.9.txt b/requirements/ubuntu-latest_py3.9.txt
index be66219ba..6f599a535 100644
--- a/requirements/ubuntu-latest_py3.9.txt
+++ b/requirements/ubuntu-latest_py3.9.txt
@@ -272,7 +272,7 @@ soupsieve==2.5
     # via beautifulsoup4
 sparse==0.15.4
     # via dscribe
-spglib==2.4.0
+spglib==2.5.2
     # via pymatgen
 sphinx==7.3.7
     # via matminer (setup.py)

From 07f9ae3abfb49363984b72d2736828b2dc7c5ce5 Mon Sep 17 00:00:00 2001
From: esoteric-ephemera <aaron.kaplan.physics@gmail.com>
Date: Fri, 23 Aug 2024 11:29:57 -0700
Subject: [PATCH 04/11] ensure correct spglib installed in requirements

---
 requirements/ubuntu-latest_py3.10.txt | 2 +-
 requirements/ubuntu-latest_py3.11.txt | 2 +-
 requirements/ubuntu-latest_py3.9.txt  | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/requirements/ubuntu-latest_py3.10.txt b/requirements/ubuntu-latest_py3.10.txt
index d01678499..86761133c 100644
--- a/requirements/ubuntu-latest_py3.10.txt
+++ b/requirements/ubuntu-latest_py3.10.txt
@@ -266,7 +266,7 @@ soupsieve==2.5
     # via beautifulsoup4
 sparse==0.15.4
     # via dscribe
-spglib==2.5.2
+spglib==2.5.0
     # via pymatgen
 sphinx==7.3.7
     # via matminer (setup.py)
diff --git a/requirements/ubuntu-latest_py3.11.txt b/requirements/ubuntu-latest_py3.11.txt
index 209088fa1..5da474efe 100644
--- a/requirements/ubuntu-latest_py3.11.txt
+++ b/requirements/ubuntu-latest_py3.11.txt
@@ -264,7 +264,7 @@ soupsieve==2.5
     # via beautifulsoup4
 sparse==0.15.4
     # via dscribe
-spglib==2.5.2
+spglib==2.5.0
     # via pymatgen
 sphinx==7.3.7
     # via matminer (setup.py)
diff --git a/requirements/ubuntu-latest_py3.9.txt b/requirements/ubuntu-latest_py3.9.txt
index 6f599a535..e5a6d6891 100644
--- a/requirements/ubuntu-latest_py3.9.txt
+++ b/requirements/ubuntu-latest_py3.9.txt
@@ -272,7 +272,7 @@ soupsieve==2.5
     # via beautifulsoup4
 sparse==0.15.4
     # via dscribe
-spglib==2.5.2
+spglib==2.5.0
     # via pymatgen
 sphinx==7.3.7
     # via matminer (setup.py)

From ace1cabbbc58be295f44806455fd48bf25e8ba1f Mon Sep 17 00:00:00 2001
From: esoteric-ephemera <aaron.kaplan.physics@gmail.com>
Date: Fri, 23 Aug 2024 13:16:15 -0700
Subject: [PATCH 05/11] add a few attempts to connect to dataset downloads in
 case internet has bad day

---
 .DS_Store                                | Bin 0 -> 6148 bytes
 docs/.DS_Store                           | Bin 0 -> 6148 bytes
 matminer/.DS_Store                       | Bin 0 -> 6148 bytes
 matminer/datasets/.DS_Store              | Bin 0 -> 6148 bytes
 matminer/datasets/tests/test_datasets.py |  11 ++++++++++-
 matminer/featurizers/.DS_Store           | Bin 0 -> 6148 bytes
 matminer/utils/.DS_Store                 | Bin 0 -> 6148 bytes
 7 files changed, 10 insertions(+), 1 deletion(-)
 create mode 100644 .DS_Store
 create mode 100644 docs/.DS_Store
 create mode 100644 matminer/.DS_Store
 create mode 100644 matminer/datasets/.DS_Store
 create mode 100644 matminer/featurizers/.DS_Store
 create mode 100644 matminer/utils/.DS_Store

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new file mode 100644
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diff --git a/docs/.DS_Store b/docs/.DS_Store
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diff --git a/matminer/.DS_Store b/matminer/.DS_Store
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diff --git a/matminer/datasets/.DS_Store b/matminer/datasets/.DS_Store
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diff --git a/matminer/datasets/tests/test_datasets.py b/matminer/datasets/tests/test_datasets.py
index 5c75dfa0c..3ba701f56 100644
--- a/matminer/datasets/tests/test_datasets.py
+++ b/matminer/datasets/tests/test_datasets.py
@@ -1,5 +1,6 @@
 import os
 import unittest
+from time import sleep
 
 import numpy as np
 import requests
@@ -20,6 +21,7 @@ def universal_dataset_check(
         numeric_headers=None,
         bool_headers=None,
         test_func=None,
+        max_connect_attempts: int = 5,
     ):
         # "Hard" integrity checks that take a long time.
         # These tests only run if the MATMINER_DATASET_FULL_TEST
@@ -75,7 +77,14 @@ def universal_dataset_check(
         # This runs when on a system with the CI environment var present
         # (e.g. when running a continuous integration VCS system)
         else:
-            download_page = requests.head(self.dataset_dict[dataset_name]["url"])
+            # try to be lenient in connecting to DB, in case a request fails once
+            for iconnect in range(max_connect_attempts):
+                download_page = requests.head(self.dataset_dict[dataset_name]["url"])
+                if download_page.ok:
+                    break
+                if iconnect < max_connect_attempts-1:
+                    sleep(5)
+                    
             self.assertTrue(download_page.ok)
 
 
diff --git a/matminer/featurizers/.DS_Store b/matminer/featurizers/.DS_Store
new file mode 100644
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diff --git a/matminer/utils/.DS_Store b/matminer/utils/.DS_Store
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From fdd527f8bac94df3086fb38af85d2d79059fc4dd Mon Sep 17 00:00:00 2001
From: esoteric-ephemera <aaron.kaplan.physics@gmail.com>
Date: Fri, 23 Aug 2024 13:17:14 -0700
Subject: [PATCH 06/11] remove mac hidden ds_stores and add to gitignore

---
 .DS_Store                      | Bin 6148 -> 0 bytes
 .gitignore                     |   2 ++
 docs/.DS_Store                 | Bin 6148 -> 0 bytes
 matminer/.DS_Store             | Bin 6148 -> 0 bytes
 matminer/datasets/.DS_Store    | Bin 6148 -> 0 bytes
 matminer/featurizers/.DS_Store | Bin 6148 -> 0 bytes
 matminer/utils/.DS_Store       | Bin 6148 -> 0 bytes
 7 files changed, 2 insertions(+)
 delete mode 100644 .DS_Store
 delete mode 100644 docs/.DS_Store
 delete mode 100644 matminer/.DS_Store
 delete mode 100644 matminer/datasets/.DS_Store
 delete mode 100644 matminer/featurizers/.DS_Store
 delete mode 100644 matminer/utils/.DS_Store

diff --git a/.DS_Store b/.DS_Store
deleted file mode 100644
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diff --git a/.gitignore b/.gitignore
index b32a3093b..d3b12e816 100644
--- a/.gitignore
+++ b/.gitignore
@@ -8,6 +8,8 @@ docs/_build/*/*/*
 # C extensions
 *.so
 
+.DS_Store
+
 # Packages
 *.egg
 *.egg-info
diff --git a/docs/.DS_Store b/docs/.DS_Store
deleted file mode 100644
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GIT binary patch
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From e442701af5a92a389f4962ac3179b7c4ed2935d5 Mon Sep 17 00:00:00 2001
From: esoteric-ephemera <aaron.kaplan.physics@gmail.com>
Date: Mon, 26 Aug 2024 09:53:17 -0700
Subject: [PATCH 07/11] precommit

---
 matminer/datasets/tests/test_datasets.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/matminer/datasets/tests/test_datasets.py b/matminer/datasets/tests/test_datasets.py
index 3ba701f56..ea3e108fb 100644
--- a/matminer/datasets/tests/test_datasets.py
+++ b/matminer/datasets/tests/test_datasets.py
@@ -82,9 +82,9 @@ def universal_dataset_check(
                 download_page = requests.head(self.dataset_dict[dataset_name]["url"])
                 if download_page.ok:
                     break
-                if iconnect < max_connect_attempts-1:
+                if iconnect < max_connect_attempts - 1:
                     sleep(5)
-                    
+
             self.assertTrue(download_page.ok)
 
 

From f12be3a181a868af6a3d24f6e1330839176d4788 Mon Sep 17 00:00:00 2001
From: esoteric-ephemera <aaron.kaplan.physics@gmail.com>
Date: Mon, 23 Sep 2024 09:06:05 -0700
Subject: [PATCH 08/11] ensure backwards compat with older spglib, loosen lower
 pin on spglib version, upper pin on numpy

---
 matminer/featurizers/structure/bonding.py | 4 ++--
 pyproject.toml                            | 2 +-
 requirements/ubuntu-latest_py3.10.txt     | 2 +-
 requirements/ubuntu-latest_py3.11.txt     | 2 +-
 requirements/ubuntu-latest_py3.9.txt      | 2 +-
 setup.py                                  | 1 -
 6 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/matminer/featurizers/structure/bonding.py b/matminer/featurizers/structure/bonding.py
index 148fda9cc..36183727f 100644
--- a/matminer/featurizers/structure/bonding.py
+++ b/matminer/featurizers/structure/bonding.py
@@ -805,8 +805,8 @@ def get_equiv_sites(self, s, site):
         sga = SpacegroupAnalyzer(s, symprec=0.01)
         sg = sga.get_space_group_operations
         sym_data = sga.get_symmetry_dataset()
-        equiv_atoms = sym_data.equivalent_atoms
-        wyckoffs = sym_data.wyckoffs
+        equiv_atoms = getattr(sym_data,"equivalent_atoms",sym_data["equivalent_atoms"])
+        wyckoffs = getattr(sym_data,"wyckoffs",sym_data["wyckoffs"])
         sym_struct = SymmetrizedStructure(s, sg, equiv_atoms, wyckoffs)
         equivs = sym_struct.find_equivalent_sites(site)
         return equivs
diff --git a/pyproject.toml b/pyproject.toml
index ce428dd9b..77d85ff41 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,7 +1,7 @@
 [build-system]
 requires = [
      # pin NumPy version used in the build
-     "numpy>=1.20.1",
+     "numpy>=1.20.1, <2",
      "setuptools>=43.0.0",
 ]
 build-backend = "setuptools.build_meta"
diff --git a/requirements/ubuntu-latest_py3.10.txt b/requirements/ubuntu-latest_py3.10.txt
index 86761133c..ab2cbb6cc 100644
--- a/requirements/ubuntu-latest_py3.10.txt
+++ b/requirements/ubuntu-latest_py3.10.txt
@@ -266,7 +266,7 @@ soupsieve==2.5
     # via beautifulsoup4
 sparse==0.15.4
     # via dscribe
-spglib==2.5.0
+spglib==2.4.0
     # via pymatgen
 sphinx==7.3.7
     # via matminer (setup.py)
diff --git a/requirements/ubuntu-latest_py3.11.txt b/requirements/ubuntu-latest_py3.11.txt
index 5da474efe..7b8853fc1 100644
--- a/requirements/ubuntu-latest_py3.11.txt
+++ b/requirements/ubuntu-latest_py3.11.txt
@@ -264,7 +264,7 @@ soupsieve==2.5
     # via beautifulsoup4
 sparse==0.15.4
     # via dscribe
-spglib==2.5.0
+spglib==2.4.0
     # via pymatgen
 sphinx==7.3.7
     # via matminer (setup.py)
diff --git a/requirements/ubuntu-latest_py3.9.txt b/requirements/ubuntu-latest_py3.9.txt
index e5a6d6891..be66219ba 100644
--- a/requirements/ubuntu-latest_py3.9.txt
+++ b/requirements/ubuntu-latest_py3.9.txt
@@ -272,7 +272,7 @@ soupsieve==2.5
     # via beautifulsoup4
 sparse==0.15.4
     # via dscribe
-spglib==2.5.0
+spglib==2.4.0
     # via pymatgen
 sphinx==7.3.7
     # via matminer (setup.py)
diff --git a/setup.py b/setup.py
index 9f9ac8faf..c0e79f2de 100644
--- a/setup.py
+++ b/setup.py
@@ -63,7 +63,6 @@ def local_version(version):
             "sympy ~= 1.11",
             "monty >= 2023",
             "pymatgen >= 2023",
-            "spglib>=2.5.0",
         ],
         extras_require=extras_require,
         classifiers=[

From 45a005a6710e9158ef322853c485ab94aa1b84a7 Mon Sep 17 00:00:00 2001
From: esoteric-ephemera <aaron.kaplan.physics@gmail.com>
Date: Mon, 23 Sep 2024 09:06:24 -0700
Subject: [PATCH 09/11] precommit

---
 matminer/featurizers/structure/bonding.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/matminer/featurizers/structure/bonding.py b/matminer/featurizers/structure/bonding.py
index 36183727f..69b1ecc9e 100644
--- a/matminer/featurizers/structure/bonding.py
+++ b/matminer/featurizers/structure/bonding.py
@@ -805,8 +805,8 @@ def get_equiv_sites(self, s, site):
         sga = SpacegroupAnalyzer(s, symprec=0.01)
         sg = sga.get_space_group_operations
         sym_data = sga.get_symmetry_dataset()
-        equiv_atoms = getattr(sym_data,"equivalent_atoms",sym_data["equivalent_atoms"])
-        wyckoffs = getattr(sym_data,"wyckoffs",sym_data["wyckoffs"])
+        equiv_atoms = getattr(sym_data, "equivalent_atoms", sym_data["equivalent_atoms"])
+        wyckoffs = getattr(sym_data, "wyckoffs", sym_data["wyckoffs"])
         sym_struct = SymmetrizedStructure(s, sg, equiv_atoms, wyckoffs)
         equivs = sym_struct.find_equivalent_sites(site)
         return equivs

From eed6f93b1bcefcdfb8fdb1beabb43648fd62939d Mon Sep 17 00:00:00 2001
From: esoteric-ephemera <aaron.kaplan.physics@gmail.com>
Date: Wed, 25 Sep 2024 10:34:35 -0700
Subject: [PATCH 10/11] repin spglib == 2.5, add read permissions for workflow
 actions (somehow GH token not being read

---
 .github/workflows/test.yml            | 3 +++
 requirements/ubuntu-latest_py3.10.txt | 2 +-
 requirements/ubuntu-latest_py3.11.txt | 2 +-
 requirements/ubuntu-latest_py3.9.txt  | 2 +-
 4 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index e362429ea..2c5d40bd3 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -3,6 +3,9 @@
 # The ext package is also only tested in this workflow. Coverage is also computed based on this platform.
 name: Testing
 
+permissions:
+  contents: read
+  
 env:
   PYTEST_ADDOPTS: "--color=yes"
 
diff --git a/requirements/ubuntu-latest_py3.10.txt b/requirements/ubuntu-latest_py3.10.txt
index ab2cbb6cc..86761133c 100644
--- a/requirements/ubuntu-latest_py3.10.txt
+++ b/requirements/ubuntu-latest_py3.10.txt
@@ -266,7 +266,7 @@ soupsieve==2.5
     # via beautifulsoup4
 sparse==0.15.4
     # via dscribe
-spglib==2.4.0
+spglib==2.5.0
     # via pymatgen
 sphinx==7.3.7
     # via matminer (setup.py)
diff --git a/requirements/ubuntu-latest_py3.11.txt b/requirements/ubuntu-latest_py3.11.txt
index 7b8853fc1..5da474efe 100644
--- a/requirements/ubuntu-latest_py3.11.txt
+++ b/requirements/ubuntu-latest_py3.11.txt
@@ -264,7 +264,7 @@ soupsieve==2.5
     # via beautifulsoup4
 sparse==0.15.4
     # via dscribe
-spglib==2.4.0
+spglib==2.5.0
     # via pymatgen
 sphinx==7.3.7
     # via matminer (setup.py)
diff --git a/requirements/ubuntu-latest_py3.9.txt b/requirements/ubuntu-latest_py3.9.txt
index be66219ba..e5a6d6891 100644
--- a/requirements/ubuntu-latest_py3.9.txt
+++ b/requirements/ubuntu-latest_py3.9.txt
@@ -272,7 +272,7 @@ soupsieve==2.5
     # via beautifulsoup4
 sparse==0.15.4
     # via dscribe
-spglib==2.4.0
+spglib==2.5.0
     # via pymatgen
 sphinx==7.3.7
     # via matminer (setup.py)

From 8f372833fb2427a790ef7af8349f511e8a3d1faf Mon Sep 17 00:00:00 2001
From: Matthew Evans <7916000+ml-evs@users.noreply.github.com>
Date: Mon, 30 Sep 2024 14:08:03 +0200
Subject: [PATCH 11/11] Update .github/workflows/test.yml

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 2c5d40bd3..7f31e5bc6 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -5,7 +5,7 @@ name: Testing
 
 permissions:
   contents: read
-  
+
 env:
   PYTEST_ADDOPTS: "--color=yes"