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Christian Faber
BioHelpers
Commits
a383b3a0
Commit
a383b3a0
authored
2 months ago
by
Christian Faber
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tests
parent
eee91bf8
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4 changed files
pixi.lock
+58
-0
58 additions, 0 deletions
pixi.lock
pixi.toml
+1
-0
1 addition, 0 deletions
pixi.toml
tests/test_bm_calc_residue_dist.py
+2
-1
2 additions, 1 deletion
tests/test_bm_calc_residue_dist.py
tests/test_bm_get_ref_coord.py
+1
-1
1 addition, 1 deletion
tests/test_bm_get_ref_coord.py
with
62 additions
and
2 deletions
pixi.lock
+
58
−
0
View file @
a383b3a0
...
...
@@ -17,6 +17,7 @@ environments:
- conda: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2025.1.31-hbcca054_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.4-h3394656_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/click-8.1.8-pyh707e725_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_1.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/comm-0.2.2-pyhd8ed1ab_1.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.3.1-py311hd18a35c_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/cycler-0.12.1-pyhd8ed1ab_1.conda
...
...
@@ -41,6 +42,7 @@ environments:
- conda: https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-11.0.1-h2c12942_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/icu-75.1-he02047a_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.6.1-pyha770c72_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/iniconfig-2.0.0-pyhd8ed1ab_1.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/ipykernel-6.29.5-pyh3099207_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/ipython-9.1.0-pyhfb0248b_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/ipython_pygments_lexers-1.1.1-pyhd8ed1ab_0.conda
...
...
@@ -126,6 +128,7 @@ environments:
- conda: https://conda.anaconda.org/conda-forge/noarch/pip-25.0.1-pyh8b19718_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/pixman-0.44.2-h29eaf8c_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/platformdirs-4.3.7-pyh29332c3_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/pluggy-1.5.0-pyhd8ed1ab_1.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/prompt-toolkit-3.0.50-pyha770c72_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/psutil-7.0.0-py311h9ecbd09_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-hb9d3cd8_1002.conda
...
...
@@ -134,6 +137,7 @@ environments:
- conda: https://conda.anaconda.org/conda-forge/noarch/pygments-2.19.1-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/pyparsing-3.2.3-pyhd8ed1ab_1.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/pyside6-6.9.0-py311h9053184_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/pytest-8.3.5-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.11.11-h9e4cc4f_2_cpython.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.9.0.post0-pyhff2d567_1.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/python-tzdata-2025.2-pyhd8ed1ab_0.conda
...
...
@@ -150,6 +154,7 @@ environments:
- conda: https://conda.anaconda.org/conda-forge/noarch/stack_data-0.6.3-pyhd8ed1ab_1.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/threadpoolctl-3.6.0-pyhecae5ae_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/tomli-2.2.1-pyhd8ed1ab_1.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/tornado-6.4.2-py311h9ecbd09_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/traitlets-5.14.3-pyhd8ed1ab_1.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.13.1-pyh29332c3_0.conda
...
...
@@ -326,6 +331,15 @@ packages:
license_family: BSD
size: 84705
timestamp: 1734858922844
- conda: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_1.conda
sha256: ab29d57dc70786c1269633ba3dff20288b81664d3ff8d21af995742e2bb03287
md5: 962b9857ee8e7018c22f2776ffa0b2d7
depends:
- python >=3.9
license: BSD-3-Clause
license_family: BSD
size: 27011
timestamp: 1733218222191
- conda: https://conda.anaconda.org/conda-forge/noarch/comm-0.2.2-pyhd8ed1ab_1.conda
sha256: 7e87ef7c91574d9fac19faedaaee328a70f718c9b4ddadfdc0ba9ac021bd64af
md5: 74673132601ec2b7fc592755605f4c1b
...
...
@@ -582,6 +596,15 @@ packages:
license_family: APACHE
size: 29141
timestamp: 1737420302391
- conda: https://conda.anaconda.org/conda-forge/noarch/iniconfig-2.0.0-pyhd8ed1ab_1.conda
sha256: 0ec8f4d02053cd03b0f3e63168316530949484f80e16f5e2fb199a1d117a89ca
md5: 6837f3eff7dcea42ecd714ce1ac2b108
depends:
- python >=3.9
license: MIT
license_family: MIT
size: 11474
timestamp: 1733223232820
- conda: https://conda.anaconda.org/conda-forge/noarch/ipykernel-6.29.5-pyh3099207_0.conda
sha256: 33cfd339bb4efac56edf93474b37ddc049e08b1b4930cf036c893cc1f5a1f32a
md5: b40131ab6a36ac2c09b7c57d4d3fbf99
...
...
@@ -1583,6 +1606,15 @@ packages:
license_family: MIT
size: 23291
timestamp: 1742485085457
- conda: https://conda.anaconda.org/conda-forge/noarch/pluggy-1.5.0-pyhd8ed1ab_1.conda
sha256: 122433fc5318816b8c69283aaf267c73d87aa2d09ce39f64c9805c9a3b264819
md5: e9dcbce5f45f9ee500e728ae58b605b6
depends:
- python >=3.9
license: MIT
license_family: MIT
size: 23595
timestamp: 1733222855563
- conda: https://conda.anaconda.org/conda-forge/noarch/prompt-toolkit-3.0.50-pyha770c72_0.conda
sha256: 0749c49a349bf55b8539ce5addce559b77592165da622944a51c630e94d97889
md5: 7d823138f550b14ecae927a5ff3286de
...
...
@@ -1673,6 +1705,23 @@ packages:
license_family: LGPL
size: 10104768
timestamp: 1743760689943
- conda: https://conda.anaconda.org/conda-forge/noarch/pytest-8.3.5-pyhd8ed1ab_0.conda
sha256: 963524de7340c56615583ba7b97a6beb20d5c56a59defb59724dc2a3105169c9
md5: c3c9316209dec74a705a36797970c6be
depends:
- colorama
- exceptiongroup >=1.0.0rc8
- iniconfig
- packaging
- pluggy <2,>=1.5
- python >=3.9
- tomli >=1
constrains:
- pytest-faulthandler >=2
license: MIT
license_family: MIT
size: 259816
timestamp: 1740946648058
- conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.11.11-h9e4cc4f_2_cpython.conda
build_number: 2
sha256: e0be7ad95a034d10e021f15317bf5c70fc1161564fa47844984c245505cde36c
...
...
@@ -1922,6 +1971,15 @@ packages:
license_family: BSD
size: 3318875
timestamp: 1699202167581
- conda: https://conda.anaconda.org/conda-forge/noarch/tomli-2.2.1-pyhd8ed1ab_1.conda
sha256: 18636339a79656962723077df9a56c0ac7b8a864329eb8f847ee3d38495b863e
md5: ac944244f1fed2eb49bae07193ae8215
depends:
- python >=3.9
license: MIT
license_family: MIT
size: 19167
timestamp: 1733256819729
- conda: https://conda.anaconda.org/conda-forge/linux-64/tornado-6.4.2-py311h9ecbd09_0.conda
sha256: afa3489113154b5cb0724b0bf120b62df91f426dabfe5d02f2ba09e90d346b28
md5: df3aee9c3e44489257a840b8354e77b9
...
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pixi.toml
+
1
−
0
View file @
a383b3a0
...
...
@@ -17,3 +17,4 @@ scikit-learn = ">=1.6.1,<2"
black
=
">
=
25.1
.
0
,
<
26
"
pandas
=
">
=
2.2
.
3
,
<
3
"
biopython
=
">
=
1.85
,
<
2
"
pytest
=
">
=
8.3
.
5
,
<
9
"
This diff is collapsed.
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tests/test_bm_calc_residue_dist.py
+
2
−
1
View file @
a383b3a0
...
...
@@ -2,6 +2,7 @@ import Bio.PDB
from
Bio.PDB.Residue
import
Residue
from
Bio.PDB.Atom
import
Atom
from
pytest
import
MonkeyPatch
,
approx
import
numpy
as
np
import
pytest
from
unittest
import
TestCase
from
src.BioHelpers_FABER.bio_mod
import
calc_residue_dist
...
...
@@ -11,7 +12,7 @@ RESIDUES = list(STRUCTURE.get_residues())
def
test_null_vectors
(
monkeypatch
:
MonkeyPatch
):
monkeypatch
.
setattr
(
Atom
,
"
get_coord
"
,
lambda
_
:
[
0
,
0
,
0
]
)
monkeypatch
.
setattr
(
Atom
,
"
get_coord
"
,
lambda
_
:
np
.
zeros
(
3
)
)
assert
calc_residue_dist
(
RESIDUES
[
5
],
RESIDUES
[
5
])
==
0.0
assert
(
calc_residue_dist
(
RESIDUES
[
5
],
RESIDUES
[
5
],
res_type
=
"
rna
"
,
reference
=
"
nearest
"
)
...
...
This diff is collapsed.
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tests/test_bm_get_ref_coord.py
+
1
−
1
View file @
a383b3a0
...
...
@@ -25,7 +25,7 @@ def test_get_ref_coord_nitrogen():
def
test_get_ref_coord_nearest
():
expected_val
=
np
.
array
([
0
,
0
,
0
],
dtype
=
np
.
float32
)
expected_val
=
np
.
array
([
20.483
,
18.827
,
16.128
],
dtype
=
np
.
float32
)
np
.
testing
.
assert_equal
(
get_reference_coordinates
(
RESIDUES
[
5
],
RESIDUES
[
5
],
reference
=
"
nearest
"
),
(
...
...
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