Trying to solve EI-CoreBioinformatics/portcullis#50

lucventurini · Jan 9, 2020 · 113065a · 113065a
1 parent 0a9adfb
commit 113065a
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Showing 3 changed files with 34 additions and 34 deletions.
diff --git a/Mikado/configuration/__init__.py b/Mikado/configuration/__init__.py
@@ -16,8 +16,8 @@
 
 def print_toml_config(output, out):
 
-    pat = re.compile("(SimpleComment|Comment)\s{0,}=\s{0,}")
-    skip_pat = re.compile("^\[(SimpleComment|Comment)\]")
+    pat = re.compile(r"(SimpleComment|Comment)s{0,}=s{0,}")
+    skip_pat = re.compile(r"^[(SimpleComment|Comment)]")
 
     initial_comment = []
     first_indent_found = False

diff --git a/Mikado/picking/picker.py b/Mikado/picking/picker.py
@@ -45,7 +45,7 @@
 import sqlite3
 import msgpack
 import fastnumbers
-from scipy import percentile
+from numpy import percentile
 logging.captureWarnings(True)
 warnings.simplefilter("always")
 try:

diff --git a/environment.yml b/environment.yml
@@ -5,38 +5,38 @@ channels:
   - intel
   - defaults
 dependencies:
-  - biopython=1.74
-  - cython=0.29.13
-  - datrie=0.8
-  - decorator=4.4.0
-  - docutils=0.15.2
-  - drmaa=0.7.9
-  - fastnumbers=2.1.1
-  - hypothesis=4.39.0
-  - jsonschema=3.0.2
-  - msgpack-python=0.6.1
-  - networkx=2.3=py_0
-  - numpy=1.17.2
-  - pandas=0.25.1
-  - pip=19.2.3
-  - pyfaidx=0.5.5.2
-  - pysam=0.15.3
+  - bioconda::portcullis>=1.2
+  - biopython>=1.74
+  - cython>=0.29.13
+  - datrie>=0.8
+  - decorator
+  - docutils
+  - drmaa
+  - fastnumbers
+  - hypothesis
+  - jsonschema
+  - msgpack-python>=0.6.1
+  - networkx>=2.3
+  - numpy>=1.17.2
+  - pandas>=0.25.1
+  - pip
+  - pyfaidx>=0.5.5.2
+  - pysam>=0.15.3
   - defaults::python>=3.6
-  - python-magic=0.4.15
-  - python-rapidjson=0.8.0
-  - pyyaml=5.1.2
-  - scikit-learn=0.21.3
-  - scipy=1.3.1
-  - six=1.12.0
-  - snakemake-minimal=5.7.0
-  - sqlalchemy=1.3.9
-  - sqlalchemy-utils=0.34.1
+  - python-magic
+  - python-rapidjson>=0.8.0
+  - pyyaml>=5.1.2
+  - scikit-learn>=0.21.3
+  - scipy>=1.3.1
+  - six>=1.12.0
+  - snakemake-minimal>=5.7.0
+  - sqlalchemy>=1.3.9
+  - sqlalchemy-utils>=0.34.1
   - sqlite
-  - tabulate=0.8.5
+  - tabulate>=0.8.5
   - wheel
-  - yaml=0.1.7
   - pip:
-    - jsonref==0.2
-    - rapidjson==1.0.0
-  - conda-forge::toml==0.10.0
-  - conda-forge::tomlkit==0.5.8
+    - jsonref>=0.2
+    - rapidjson>=1.0.0
+  - conda-forge::toml>=0.10.0
+  - conda-forge::tomlkit>=0.5.8