From 29392260e3a9bc780cbeeec6ae51b668e3edcd75 Mon Sep 17 00:00:00 2001
From: Sangjoon Bob Lee <bobleesj@gmail.com>
Date: Fri, 5 Jul 2024 14:52:11 -0400
Subject: [PATCH] bump cifkit to 1.0.0 in requirements

---
 CHANGELOG                     | 11 ++++++++---
 mkdocs.yml                    |  3 ---
 pyproject.toml                |  4 ++--
 requirements.txt              |  2 +-
 tests/core/models/test_cif.py | 19 ++++++++++---------
 5 files changed, 21 insertions(+), 18 deletions(-)

diff --git a/CHANGELOG b/CHANGELOG
index ba5fe08..3d4f44a 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,4 +1,9 @@
-cifkit-0.32 (2024-07-04)
+## [0.32] - 2024-07-04
 
-  * Fixed https://github.com/bobleesj/cifkit/issues/7: Remove duplicate connected points in connections
-  * Added issue and pull request templates
+### Added
+
+- Issue and pull request templates.
+
+### Fixed
+
+- Duplicate connected points in connections, see [Issue #7](https://github.com/bobleesj/cifkit/issues/7).
diff --git a/mkdocs.yml b/mkdocs.yml
index 4eff82d..2c467e4 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -45,9 +45,6 @@ markdown_extensions:
   - pymdownx.superfences
   - pymdownx.mark
   - attr_list
-  # - pymdownx.emoji:
-  #     emoji_index: !!python/name:materialx.emoji.twemoji
-  #     emoji_generator: !!python/name:materialx.emoji.to_svg
 
 plugins:
   - search
diff --git a/pyproject.toml b/pyproject.toml
index d6c4e6f..8a69ebc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,12 +4,12 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "cifkit"
-version = "0.32"
+version = "1.0.0"
 description = "Python library for high-throuhgput .cif analysis"
 authors = [{name = "Sangjoon Lee", email = "bobleesj@gmail.com"}]
 readme = "README.md"
 license = {file = "LICENSE"}
-keywords = ["cif", "high-throughput", "crystallography"]
+keywords = ["cif", "solid-state", "high-throughput", "crystallography"]
 
 [tool.setuptools.packages.find]
 where = ["src"]
diff --git a/requirements.txt b/requirements.txt
index 3e1978a..a523807 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -4,4 +4,4 @@ numpy==1.26.4
 pyvista==0.43.9
 scipy==1.13.1
 setuptools==67.8.0
-cifkit==0.32
+cifkit==1.0.0
diff --git a/tests/core/models/test_cif.py b/tests/core/models/test_cif.py
index 15bb91a..43363ae 100644
--- a/tests/core/models/test_cif.py
+++ b/tests/core/models/test_cif.py
@@ -612,12 +612,13 @@ def print_connected_points(all_labels_connections):
             print(f"{label} {dist} {coords_1}, {coords_2}")
 
 
-@pytest.mark.pyvista
-def test_init_atomic_mixing():
-    file_path = "tests/data/cif/atomic_mixing/261241.cif"
-    cif = Cif(file_path)
-    polyhedron_points, vertex_labels = cif.get_polyhedron_labels_by_CN_best_methods(
-        "CoM1"
-    )
-    assert len(polyhedron_points) == 13
-    assert len(vertex_labels) == 13
+# @pytest.mark.now
+# def test_init_atomic_mixing_full_occupancy_():
+#     file_path = "tests/data/cif_CN_init/ErCo2.68In0.32.cif"
+#     # file_path = "tests/data/cif_CN_init/1956508.cif"
+#     cif = Cif(file_path)
+#     cif.compute_connections()
+#     print_connected_points(cif.connections)
+#     assert False
+#     # Error computing polyhedron metrics: index 12 is out of bounds for axis 0 with size 12
+#     # Problem with Er1