From 5cf298e69d82742d9765394843e458dcffc93eff Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Mon, 22 Jan 2024 10:21:18 +0100
Subject: [PATCH] progress on #236 NGSpeciesID

---
 236_NGSpeciesID/Biopython-1.83-foss-2023a.eb  | 45 -------------------
 236_NGSpeciesID/WhatsHap-2.1-foss-2023a.eb    |  9 ++--
 236_NGSpeciesID/edlib-1.3.9-GCC-12.3.0.eb     |  1 +
 ...ntervaltree-python-3.1.0-GCCcore-12.3.0.eb |  1 +
 4 files changed, 5 insertions(+), 51 deletions(-)
 delete mode 100644 236_NGSpeciesID/Biopython-1.83-foss-2023a.eb

diff --git a/236_NGSpeciesID/Biopython-1.83-foss-2023a.eb b/236_NGSpeciesID/Biopython-1.83-foss-2023a.eb
deleted file mode 100644
index 4c021941..00000000
--- a/236_NGSpeciesID/Biopython-1.83-foss-2023a.eb
+++ /dev/null
@@ -1,45 +0,0 @@
-##
-# Author:    Robert Mijakovic <robert.mijakovic@lxp.lu>
-##
-easyblock = 'PythonPackage'
-
-name = 'Biopython'
-version = '1.83'
-
-homepage = 'https://www.biopython.org'
-description = """Biopython is a set of freely available tools for biological
- computation written in Python by an international team of developers. It is
- a distributed collaborative effort to develop Python libraries and
- applications which address the needs of current and future work in
- bioinformatics. """
-
-toolchain = {'name': 'foss', 'version': '2023a'}
-
-source_urls = ['https://biopython.org/DIST']
-sources = [SOURCELOWER_TAR_GZ]
-checksums = ['78e6bfb78de63034037afd35fe77cb6e0a9e5b62706becf78a7d922b16ed83f7']
-
-dependencies = [
-    ('Python', '3.11.3'),
-    ('SciPy-bundle', '2023.07'),
-]
-
-download_dep_fail = True
-use_pip = True
-sanity_pip_check = True
-
-# Run only tests that don't require internet connection
-runtest = 'python setup.py test --offline'
-
-sanity_check_paths = {
-    'files': [],
-    'dirs': ['lib/python%(pyshortver)s/site-packages/Bio',
-             'lib/python%(pyshortver)s/site-packages/BioSQL']
-}
-
-# extra check to ensure numpy dependency is available
-sanity_check_commands = ["python -c 'import Bio.MarkovModel'"]
-
-options = {'modulename': 'Bio'}
-
-moduleclass = 'bio'
diff --git a/236_NGSpeciesID/WhatsHap-2.1-foss-2023a.eb b/236_NGSpeciesID/WhatsHap-2.1-foss-2023a.eb
index 81816394..6e425f29 100644
--- a/236_NGSpeciesID/WhatsHap-2.1-foss-2023a.eb
+++ b/236_NGSpeciesID/WhatsHap-2.1-foss-2023a.eb
@@ -12,7 +12,7 @@ especially suitable for long reads, but works also well with short reads."""
 
 toolchain = {'name': 'foss', 'version': '2023a'}
 
-# builddependencies = [('Python-bundle-PyPI', '2023.06')]
+builddependencies = [('hatchling', '1.18.0')]
 
 dependencies = [
     ('Python', '3.11.3'),
@@ -29,12 +29,9 @@ sanity_pip_check = True
 use_pip = True
 
 exts_list = [
-    ('isal', '1.5.3', {
-        'checksums': ['01d9b76db3535374d720a06f5d66031f74e609698f0382fdd6ab3a0351210b72'],
-    }),
-    ('xopen', '1.8.0', {
+    ('xopen', '1.7.0', {
         'source_tmpl': SOURCE_PY3_WHL,
-        'checksums': ['e151a23bcaa0913e9683654c197d1da2444d4e59f27aa17e93bbf42eb4a72d7d'],
+        'checksums': ['c4c6c978bb5f6f2a4364438da09f4f8fde078b6df4de18e3f72fccc472d1ee33'],
     }),
     ('PuLP', '2.8.0', {
         'source_tmpl': SOURCE_PY3_WHL,
diff --git a/236_NGSpeciesID/edlib-1.3.9-GCC-12.3.0.eb b/236_NGSpeciesID/edlib-1.3.9-GCC-12.3.0.eb
index 87cdf99d..beab29cd 100644
--- a/236_NGSpeciesID/edlib-1.3.9-GCC-12.3.0.eb
+++ b/236_NGSpeciesID/edlib-1.3.9-GCC-12.3.0.eb
@@ -13,6 +13,7 @@ checksums = ['64c3dfab3ebe3e759565a0cc71eb4df23cf3ce1713fd558af3c473dddc2a3766']
 
 dependencies = [
     ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
 ]
 
 download_dep_fail = True
diff --git a/236_NGSpeciesID/intervaltree-python-3.1.0-GCCcore-12.3.0.eb b/236_NGSpeciesID/intervaltree-python-3.1.0-GCCcore-12.3.0.eb
index cd94d62e..6e774dc9 100644
--- a/236_NGSpeciesID/intervaltree-python-3.1.0-GCCcore-12.3.0.eb
+++ b/236_NGSpeciesID/intervaltree-python-3.1.0-GCCcore-12.3.0.eb
@@ -22,6 +22,7 @@ builddependencies = [('binutils', '2.40')]
 
 dependencies = [
     ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
 ]
 
 use_pip = True