#214 add scib-metrics + pertpy

vscentrum · Jun 4, 2024 · c0938b4 · c0938b4
1 parent 3c34836
commit c0938b4
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Showing 3 changed files with 107 additions and 42 deletions.
diff --git a/214_Single-cell_python_bundle/bundle.eb b/214_Single-cell_python_bundle/bundle.eb
@@ -22,7 +22,6 @@ dependencies = [
     ('Seaborn', '0.13.2'),
     ('PyTorch', '2.1.2'),
     ('scanpy', '1.9.8'),
-    # scib-metrics TODO
     ('scib', '1.1.4'),
     ('scVelo', '0.3.1'),  # imports loompy
     ('CellTypist', '1.6.2'),
@@ -37,6 +36,7 @@ dependencies = [
     ('Cassiopeia', '2.0.0'),
     ('scvi-tools', '1.1.2'),
     ('scArches', '0.6.1'),
+    ('scib-metrics', '0.5.1'),
     # deps for exts:
     ('umap-learn', '0.5.5'),  # bbknn
     ('scikit-learn', '1.3.1'),  # bbknn, sc_toolbox
@@ -45,6 +45,7 @@ dependencies = [
     ('adjustText', '1.1.1'),  # sc_toolbox, created
     ('python-parasail', '1.3.4'),  # scirpy
     ('graph-tool', '2.59'),  # schist
+    ('Pyomo', '6.7.3'),  # pertpy
 ]
 
 # DEPS to add:
@@ -65,19 +66,12 @@ dependencies = [
     # arrow 1.3.0 requires types-python-dateutil OK exts
 # Altair OK
     # altair 5.2.0 requires toolz OK exts
-# Pertpy NO - needs scvi-tools
-    # pertpy 0.6.0 requires decoupler, which is not installed. -> Do decoupler first
-    # pertpy 0.6.0 requires ipywidgets, which is not installed.
-    # pertpy 0.6.0 requires muon, which is not installed.
-    # pertpy 0.6.0 requires numpyro, which is not installed.
-    # pertpy 0.6.0 requires ott-jax, which is not installed.
-    # pertpy 0.6.0 requires plotnine, which is not installed.
-    # pertpy 0.6.0 requires scvi-tools, which is not installed.
-    # pertpy 0.6.0 requires sparsecca, which is not installed.
-    # pertpy 0.6.0 requires toytree OK exts
-    # ('pertpy', '0.6.0', {
-    #     'checksums': ['0f9ed443a74a07ab8cd0fb6d2d06275df30ec836c161124b83c9505b7cab182b'],
-    # }),
+# Pertpy
+    # pertpy 0.6.0 requires ott-jax, ok exts
+    # pertpy 0.6.0 requires sparsecca, ok exts
+    # ott-jax 0.4.6 requires jaxopt ok exts
+    # ott-jax 0.4.6 requires lineax ok exts
+    # sparsecca 0.3.1 requires pyomo -> created OK
 # tascCODA OK
     # tasccoda 0.1.3 requires tensorflow-probability OK in scCoda -> delete TF-prob. from setup.py as in scCoda
         # strip out tensorflow-probability as required dependency, to ensure that 'pip check' passes
@@ -144,7 +138,7 @@ dependencies = [
     # should be ok in exts
     # ('decoupler', '1.6.0'),
 # contrastiveVI
-# Schist
+# Schist OK
     # not has pipy source -> github
     # missing graph_tool -> create
         # graph_tool.all.Graph
@@ -314,6 +308,21 @@ exts_list = [
         'source_urls': ['https://github.com/dawe/schist/archive/'],
         'checksums': ['9b98ec9d85554573288c24f18c4791ba7c4d315397cbc422ea25d4a7cdd42e6d'],
     }),
+    ('lineax', '0.0.5', {
+        'checksums': ['ed41098dbd94b639287f15682e19cd9ec1dc9ecad6844ee861536044a0e3285c'],
+    }),
+    ('jaxopt', '0.8.3', {
+        'checksums': ['4b06dfa6f915a4f3291699606245af6069371a48dc5c92d4c507840d62990646'],
+    }),
+    ('ott_jax', '0.4.6', {
+        'checksums': ['bc91f8d512cdb344439f5584712d76cd0650b6716b6686d53b828cc67abdbcba'],
+    }),
+    ('sparsecca', '0.3.1', {
+        'checksums': ['be1526baebac5ce6efbc7190fd62a1cec13288c493f5d427024f66ca6afaec13'],
+    }),
+    ('pertpy', '0.6.0', {
+        'checksums': ['0f9ed443a74a07ab8cd0fb6d2d06275df30ec836c161124b83c9505b7cab182b'],
+    }),
 ]
 
 use_pip = True

diff --git a/214_Single-cell_python_bundle/pyomo.eb b/214_Single-cell_python_bundle/pyomo.eb
@@ -0,0 +1,34 @@
+easyblock = 'PythonBundle'
+
+name = 'Pyomo'
+version = '6.7.3'
+
+homepage = 'https://www.pyomo.org/'
+description = """ Pyomo is a Python-based open-source software package that supports a diverse set of optimization
+ capabilities for formulating and analyzing optimization models. """
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('mpi4py', '3.1.4'),
+    ('PLY', '3.11'),
+]
+
+exts_list = [
+    ('PyUtilib', '6.0.0', {
+        'preinstallopts': """sed -i "s/'nose',//g" setup.py && """,
+        'checksums': ['d3c14f8ed9028a831b2bf51b8ab7776eba87e66cfc58a06b99c359aaa640f040'],
+    }),
+    (name, version, {
+        'checksums': ['b7f0441c405af4f42f38527ae38826a5c0a4984dd7bea1fe07172789d8594770'],
+    }),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+sanity_check_commands = ['pyomo -h']
+
+moduleclass = 'math'
diff --git a/...ython_bundle/scib-metrics-x-foss-2023a.eb → ...n_bundle/scib-metrics-0.5.1-foss-2023a.eb b/...ython_bundle/scib-metrics-x-foss-2023a.eb → ...n_bundle/scib-metrics-0.5.1-foss-2023a.eb
@@ -8,38 +8,41 @@ description = "Accelerated and Python-only metrics for benchmarking single-cell
 
 toolchain = {'name': 'foss', 'version': '2023a'}
 
+builddependencies = [
+    ('hatchling', '1.18.0'),
+    ('poetry', '1.5.1'),
+]
 dependencies = [
     ('Python', '3.11.3'),
     ('SciPy-bundle', '2023.07'),
     ('anndata', '0.10.5.post1'),
-    # ('matplotlib', '3.4.2'),
-    # ('jax', '0.3.9'),
-    # ('scikit-learn', '0.24.2'),
-    # ('anndata', '0.9.2'),
-    # ('python-igraph', '0.9.6'),
-    # ('scanpy', '1.8.1'),
-    # ('tqdm', '4.61.2'),
-    # ('dm-tree', '0.1.6'),
+    ('jax', '0.4.25'),
+    ('scikit-learn', '1.3.1'),
+    ('scanpy', '1.9.8'),
+    ('python-igraph', '0.11.4'),
+    ('matplotlib', '3.7.2'),
+    ('tqdm', '4.66.1'),
+    ('umap-learn', '0.5.5'),
 ]
 
     # "anndata", OK
-    # "chex",
-    # "jax",
-    # "jaxlib",
-    # "numpy",
-    # "pandas",
-    # "scipy",
-    # "scikit-learn",
-    # "scanpy>=1.9",
-    # "rich",
-    # "pynndescent",
-    # "igraph>0.9.0",
-    # "matplotlib",
-    # "plottable",
-    # "tqdm",
-    # "umap-learn>=0.5.0",
+    # "chex", ok exts
+    # "jax", OK
+    # "jaxlib", OK in jax
+    # "numpy", OK
+    # "pandas", OK
+    # "scipy", OK
+    # "scikit-learn", OK
+    # "scanpy>=1.9", OK
+    # "rich", ok exts
+    # "pynndescent", ok exts
+    # "igraph>0.9.0", OK
+    # "matplotlib", OK
+    # "plottable", ok exts
+    # "tqdm", OK
+    # "umap-learn>=0.5.0", OK
 
-# use_pip = True
+use_pip = True
 
 # # avoid hatchling requirement to install scib-metrics
 # local_preinstallopts_scib_metrics = """sed -i -e 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' """
@@ -48,8 +51,27 @@ dependencies = [
 # local_preinstallopts_scib_metrics += "-e '/igraph/d' pyproject.toml && "
 
 exts_list = [
-    ('chex', '0.1.85'),
+    ('toolz', '0.12.1', {
+        'checksums': ['ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d'],
+    }),
+    ('plottable', '0.1.5', {
+        'checksums': ['235d762a31c82129dc5bf74205c103a14b1e4393d0f921cc0231be5de884041d'],
+    }),
+    ('pynndescent', '0.5.11', {
+        'checksums': ['6f44ced9d5a9da2c87d9b2fff30bb5308540c0657605e4d5cde7ed3275bbad50'],
+    }),
+    ('rich', '13.7.1', {
+        'checksums': ['9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432'],
+    }),
+    ('chex', '0.1.86', {
+        'checksums': ['e8b0f96330eba4144659e1617c0f7a57b161e8cbb021e55c6d5056c7378091d1'],
+    }),
+    (name, version, {
+        'sources': ['scib_metrics-%(version)s.tar.gz'],
+        'checksums': ['74d10251acf1c11402b994faf063e55317881d7950fb78f6cef011d232a1e266'],
+    }),
 ]
+
 #     # more recent setuptools required because scib-metrics uses pyproject.toml
 #     ('setuptools', '68.1.2', {
 #         'checksums': ['3d4dfa6d95f1b101d695a6160a7626e15583af71a5f52176efa5d39a054d475d'],
@@ -87,6 +109,6 @@ exts_list = [
 #     }),
 # ]
 
-# sanity_pip_check = True
+sanity_pip_check = True
 
-# moduleclass = 'bio'
+moduleclass = 'bio'