bioconda recipe; fix str cast when profiles are user-defined

bioconda-recipes-nordic/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright © 2023 Clémence Réda
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

bioconda-recipes-nordic/build.sh

@@ -0,0 +1,23 @@
+#!/usr/bin/env bash
+
+cd ${SRC_DIR}"/MaBoSS-2.0/engine/src/"
+
+make install \
+    CC="${CC}" \
+    CXX="${CXX}" \
+    CFLAGS="${CFLAGS}" \
+    CXXFLAGS="${CXXFLAGS}" \
+    LDFLAGS="${LDFLAGS}" \
+    prefix="${PREFIX}"
+
+cd ${SRC_DIR}"/mpbn-3.3/"
+
+"${PYTHON}" -m pip install --no-deps --no-build-isolation . -vvv
+
+cd ${SRC_DIR}"/bonesis-0.5.7/"
+
+"${PYTHON}" -m pip install --no-deps --no-build-isolation . -vvv
+
+cd ${SRC_DIR}"/NORDic-2.4.4/"
+
+"${PYTHON}" -m pip install --no-deps --no-build-isolation . -vvv

bioconda-recipes-nordic/meta.yaml

@@ -0,0 +1,92 @@
+{% set name = "nordic" %}
+{% set ucname = "NORDic" %}
+{% set version = "2.4.4" %}
+
+package:
+  name: "{{ name|lower }}"
+  version: "{{ version }}"
+
+source:
+  - url: "https://github.com/sysbio-curie/MaBoSS-env-2.0/archive/refs/heads/master.tar.gz"
+    sha256: 5952813f3c38e10bbc2f0d4bbb91936bc738c47bcf9941da298cea3bfb753d19
+    folder: "MaBoSS-2.0"
+  - url: "https://files.pythonhosted.org/packages/f8/ff/4b5fd3c1968c99d59972da395c926be65e601d7306602ec6cc39c418e24f/mpbn-3.3.tar.gz"
+    sha256: 8831531216d94616e7303925c4571bfc40f5d750b33b69d0155edc8404223831
+    folder: "mpbn-3.3"
+  - url: "https://files.pythonhosted.org/packages/fb/c9/8fa247a95e6d6b7c650f2d4f879e6027fbb9eeca2aaba8d97f999bfadcfd/bonesis-0.5.7.tar.gz"
+    sha256: 0ccef4daa089347f7fd4ac8355f7ab3a8eecf63757e6bf000cc66b7c54bfdb0a
+    folder: "bonesis-0.5.7"
+  - url: "https://files.pythonhosted.org/packages/f3/9b/817e2004a1e7f798b5f361dc04d28d7b99657cc469f26abde2d9095fd1e4/{{ ucname }}-{{ version }}.tar.gz"
+    sha256: 01a5d9fbc95c603e46e916a734dd6eecdc20dff914d36c91009337d62488d525
+    folder: "{{ ucname }}-{{ version }}"
+
+build:
+  number: 0
+  skip: True  # [py < 38]
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x") }}
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+    - flex
+    - bison
+    - make
+  host:
+    - python
+    - pip
+    - clingo >=5.6.1
+    - cmappy
+    - scikit-learn
+    - graphviz
+    - matplotlib-base
+    - numpy >=1.22.4
+    - omnipath >=1.0.6
+    - openpyxl >=3.0.10
+    - pandas >=1.5.1
+    - qnorm >=0.5.1
+    - quadprog >=0.1.11
+    - scipy >=1.6.2
+    - seaborn >=0.12.1
+    - tqdm >=4.62.3
+  run:
+    - python
+    - clingo >=5.6.1
+    - cmappy
+    - scikit-learn
+    - graphviz
+    - matplotlib-base
+    - numpy >=1.22.4
+    - omnipath >=1.0.6
+    - openpyxl >=3.0.10
+    - pandas >=1.5.1
+    - qnorm >=0.5.1
+    - quadprog >=0.1.11
+    - scipy >=1.6.2
+    - seaborn >=0.12.1
+    - tqdm >=4.62.3
+
+test:
+  imports:
+    - NORDic
+    - NORDic.NORDic_DR
+    - NORDic.NORDic_DS
+    - NORDic.NORDic_NI
+    - NORDic.NORDic_PMR
+    - NORDic.UTILS
+
+about:
+  home: "https://github.com/clreda/NORDic"
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  summary: "NORDic: a Network-Oriented package for the Repurposing of Drugs"
+  doc_url: "https://github.com/clreda/NORDic/blob/main/README.md"
+  dev_url: "https://github.com/clreda/NORDic"
+
+extra:
+  recipe-maintainers:
+    - clreda
+  identifiers:
+    - doi:10.5281/zenodo.7239047

src/NORDic/NORDic_NI/functions.py

@@ -377,7 +377,7 @@ def solution_generation(file_folder, taxon_id, path_to_genes=None, disgenet_args
 
     profiles = pd.read_csv(profiles_fname, index_col=0, low_memory=False)
     if (not pd.isnull(profiles.values).all()):
-        nconds = len(set(["_".join([profiles.loc[v][c] for v in ["perturbed","perturbation","cell_line"]]) for c in profiles.columns]))
+        nconds = len(set(["_".join([str(profiles.loc[v][c]) for v in ["perturbed","perturbation","cell_line"]]) for c in profiles.columns]))
     else:
         nconds = 0
     ngenes = len([p for p in profiles.index if (p not in add_rows_profiles)])