From 29b82676a5df7fc316a5b5c080ed1916be0ebc86 Mon Sep 17 00:00:00 2001
From: Eric Wong <eyssen1023@gmail.com>
Date: Wed, 8 Jan 2025 14:11:55 +0800
Subject: [PATCH] add cryolo 1.9.9

---
 .../c/cryolo/cryolo-1.9.9-foss-2022a.eb       | 39 +++++++++++++++++++
 .../fix_cryolo_gui_no_attribute_version.patch | 14 +++++++
 .../c/cryolo/requirements-1.9.9.txt           | 37 ++++++++++++++++++
 3 files changed, 90 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/cryolo/cryolo-1.9.9-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/c/cryolo/fix_cryolo_gui_no_attribute_version.patch
 create mode 100644 easybuild/easyconfigs/c/cryolo/requirements-1.9.9.txt

diff --git a/easybuild/easyconfigs/c/cryolo/cryolo-1.9.9-foss-2022a.eb b/easybuild/easyconfigs/c/cryolo/cryolo-1.9.9-foss-2022a.eb
new file mode 100644
index 00000000000..8583d5bb5f4
--- /dev/null
+++ b/easybuild/easyconfigs/c/cryolo/cryolo-1.9.9-foss-2022a.eb
@@ -0,0 +1,39 @@
+easyblock = 'PythonPackage'
+
+name = 'cryolo'
+version = '1.9.9'
+
+homepage = 'https://cryolo.readthedocs.io/'
+
+description = """an application for fast and accurate cryo-EM particle picking. 
+It’s based on convolutional neural networks and utilizes the popular You Only Look Once (YOLO) object detection system."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+# this is a bundle of Python packages
+exts_defaultclass = 'PythonPackage'
+
+dependencies = [
+    ('Python', '3.8.10'),
+    ('LibTIFF', '4.3.0'),
+    ('GTK3', '3.24.33'),
+]
+
+multi_deps_load_default = False
+installopts = '--no-index'
+sources = ['requirements-%(version)s.txt']
+patches = ['fix_cryolo_gui_no_attribute_version.patch']
+checksums = [
+    'c1d6b4161875fbe7553578c5d1eebc58db8a5977c9db488c0ef9e6fbc3b75f6a',
+    'f3bc9feb225293d2608c40c9a33c8d1177c1243f610acb18f16ad1bc4e500382'
+]
+
+
+unpack_sources = False
+use_pip = True
+use_pip_for_deps = True
+use_pip_requirement = True
+fix_python_shebang_for = ['bin/*']
+sanity_pip_check = True
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/c/cryolo/fix_cryolo_gui_no_attribute_version.patch b/easybuild/easyconfigs/c/cryolo/fix_cryolo_gui_no_attribute_version.patch
new file mode 100644
index 00000000000..95fff6d7acf
--- /dev/null
+++ b/easybuild/easyconfigs/c/cryolo/fix_cryolo_gui_no_attribute_version.patch
@@ -0,0 +1,14 @@
+# fix AttributeError: module 'cryolo.__init__' has no attribute '__version__'
+# Author: Eric Wong
+
+--- lib/python3.8/site-packages/cryolo/cryolo_main.py.old	2025-01-07 14:25:10.536352020 +0800
++++ lib/python3.8/site-packages/cryolo/cryolo_main.py	2025-01-07 14:28:18.826209903 +0800
+@@ -461,7 +461,7 @@
+ 
+     Gooey(
+         main,
+-        program_name="crYOLO " + ini.__version__,
++        program_name="crYOLO " + getattr(ini, '__version__', getattr(ini, 'version', '1.9.9')),
+         image_dir=os.path.join(os.path.abspath(os.path.dirname(__file__)), "../icons"),
+         progress_regex=r"^.* \( Progress:\s+(-?\d+) % \)$",
+         disable_progress_bar_animation=True,
diff --git a/easybuild/easyconfigs/c/cryolo/requirements-1.9.9.txt b/easybuild/easyconfigs/c/cryolo/requirements-1.9.9.txt
new file mode 100644
index 00000000000..6a0b4fe81b8
--- /dev/null
+++ b/easybuild/easyconfigs/c/cryolo/requirements-1.9.9.txt
@@ -0,0 +1,37 @@
+--index-url https://mirrors.aliyun.com/pypi/simple/
+--extra-index-url https://pypi.ngc.nvidia.com
+setuptools<66
+pip
+Brotli==1.1.0
+certifi==2024.8.30
+cffi==1.17.0
+charset-normalizer==3.4.0
+h2==4.1.0
+hpack==4.0.0
+hyperframe==6.0.1
+idna==3.10
+numpy==1.18.5
+scikit-image==0.19.3
+scikit-learn==0.23.2
+scipy==1.9.3
+tifffile==2020.9.3
+imageio==2.15.0
+packaging==24.2
+pathlib2==2.3.7.post1
+Pillow==9.4.0
+ply==3.11
+pycparser==2.22
+Pypubsub==4.0.3
+PyQt5==5.15.7
+PyQt5-sip==12.11.0
+PySocks==1.7.1
+requests==2.32.3
+sip==6.7.12
+six==1.16.0
+toml==0.10.2
+tomli==2.0.2
+urllib3==2.2.3
+wheel==0.45.1
+wxPython==4.1.1
+zstandard==0.23.0
+cryolo[c11]==1.9.9