feat: harmonise conda dependencies and installation

pyproject.toml

@@ -1,2 +1,2 @@
 [build-system]
-requires = ["Cython", "numpy~=1.20.3", "setuptools", "wheel"]
+requires = ["Cython", "numpy~=1.23.3", "setuptools", "wheel"]

reat.yml

@@ -1,16 +1,102 @@
 name: REAT
 channels:
-  - conda-forge
   - bioconda
+  - conda-forge
+  - defaults
+  - anaconda
 dependencies:
-  - pip
+  - python>=3.9,<3.11
+  - appdirs=1.4.4
+  - attrs=22.1.0
+  - biopython=1.79
+  - brotlipy=0.7.0
+  - bumpversion=0.5.3
+  - certifi=2022.9.24
+  - cffi=1.15.1
+  - charset-normalizer=2.1.1
+  - click=8.1.3
+  - click-log=0.4.0
+  - colorama=0.4.5
+  - conda=22.9.0
+  - conda-package-handling=1.9.0
+  - ConfigArgParse=1.5.3
+  - cryptography=37.0.1
+  - Cython=0.29.32
+  - datrie=0.8.2
+  - docutils=0.19
+  - drmaa=0.7.9
+  - exceptiongroup=1.0.0rc9
+  - filelock=3.8.0
+  - gitdb=4.0.9
+  - GitPython=3.1.29
+  - greenlet=1.1.3.post0
+  - hypothesis=6.56.2
+  - idna=3.4
+  - iniconfig=1.1.1
+  - joblib=1.2.0
+  - jsonschema=3.2.0
+  - libmambapy=0.27.0
+  - marshmallow=3.14.1
+  - marshmallow-dataclass=8.5.3
+  - msgpack-python==1.0.4
+  - nbformat=5.7.0
+  - ncls=0.0.65
+  - networkx=2.8.7
+  - numpy=1.23.3
+  - packaging=21.3
+  - pandas=1.5.0
+  - pip=22.2.2
+  - pluggy=1.0.0
+  - psutil=5.9.2
+  - PuLP=2.6.0
+  - py=1.11.0
+  - pycosat=0.6.3
+  - pycparser=2.21
+  - pyfaidx=0.5.9.5
+  - pyOpenSSL=22.0.0
+  - pyparsing=3.0.9
+  - pyrsistent=0.18.1
+  - pysam=0.19.1
+  - PySocks=1.7.1
+  - pytest=7.1.3
+  - python-dateutil=2.8.2
+  - python-rapidjson=1.9
+  - pytz=2022.4
+  - PyVCF3=1.0.3
+  - PyYAML=6.0.1
+  - requests=2.28.1
+  - scikit-learn=1.1.2
+  - scipy=1.11.1
+  - setuptools=65.4.1
+  - six=1.16.0
+  - smart-open=6.2.0
+  - snakemake=6.15.5
+  - sortedcontainers=2.4.0
+  - SQLAlchemy=1.4.41
+  - SQLAlchemy-Utils=0.38.3
+  - stopit=1.1.2
+  - tabulate=0.9.0
+  - threadpoolctl=3.1.0
+  - toml=0.10.2
+  - tomli=2.0.1
+  - toolz=0.12.0
+  - toposort=1.7
+  - tqdm=4.64.1
+  - traitlets=5.4.0
+  - typeguard=2.13.3
+  - typing_extensions=4.4.0
+  - wheel=0.37.1
+  - wrapt=1.14.1
+  - samtools>=1.11
+  - htslib>=1.11
+  - prodigal==2.6.3
+  - diamond==2.0.11
+  - portcullis==1.2.4
   - git=2.26.0
   - gnuplot=5.4.1
   - libjpeg-turbo=2.1.0
   - bioawk=1.0
   - seqkit=0.16.1
-  - samtools=1.12
-  - portcullis=1.2.4
   - stringtie=2.1.5
   - hisat2=2.2.1
   - minimap2=2.18
@@ -21,9 +107,7 @@ dependencies:
   - gffread=0.12.1
   - seqtk=1.3
   - transdecoder=5.5.0
-  - prodigal=2.6.3
   - blast>=2.9.0
-  - diamond>=2.0.0
   - scallop-lr=0.9.2
   - bedtools=2.30.0
   - ucsc-wigtobigwig=377
@@ -32,3 +116,5 @@ dependencies:
   - codingquarry=2.0
   - augustus=3.4.0
   - evidencemodeler=1.1.1
+  - miniprot=0.12
+

setup.py

@@ -36,11 +36,6 @@
     ),
     scripts=[script for script in glob.glob("annotation/scripts/*")],
     install_requires=[
-        "biopython~=1.78",
-        "mikado~=2.3.4",
-        "pyfaidx~=0.5.8",
-        "jsonschema~=3.2.0",
-        "pyyaml~=5.4.1",
         "parasail~=1.2.4",
         "2passtools @ git+https://github.com/bartongroup/2passtools.git#d4378d0",
     ],