diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..a06b7a6debe656435c7be37a8cc056bda5b941ce --- /dev/null +++ b/requirements.txt @@ -0,0 +1,25 @@ +backports +backports.functools_lru_cache +backports_abc +cycler +libwebp-base +lz4-c +matplotlib +numpy +openssl +pandas +patsy +pillow +pip +pyparsing +python3.6 +python-dateutil +python_abi +pytz +readline +reportlab +scikit-learn +scipy +setuptools +statsmodels +tk \ No newline at end of file diff --git a/setup.cfg b/setup.cfg index 98c4b582c569fbe1126d8d0cbe66e0202a0a474a..5ab250f58e558274234932761e131074cb2c725c 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,18 +1,20 @@ [metadata] -name = phageTerm -version = 4.1 +name = phageTermVirome +version = 2.0 author = Marc Monot author_email = marc.monot@pasteur.fr description = Using sequencing bias to identify phages terminii and phage genome packaging. long_description = file: README.txt -long_description_content_type = text +long_description_content_type = text/plain url = https://gitlab.pasteur.fr/vlegrand/ptv project_urls = Bug Tracker = https://gitlab.pasteur.fr/vlegrand/ptv/-/issues classifiers = Programming Language :: Python :: 3 - License :: OSI Approved :: GNU AFFERO GENERAL PUBLIC LICENSE, Version 3, 19 November 2007 + License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+) Operating System :: OS Independent + Development Status :: 5 - Production/Stable +platforms=any [options] package_dir = @@ -21,4 +23,47 @@ packages = find: python_requires = >=3.6 [options.packages.find] -where = . \ No newline at end of file +where = . + +install_requires = + backports + backports.functools_lru_cache + backports_abc + cycler + libwebp-base + lz4-c + matplotlib + numpy + openssl + pandas + patsy + pillow + pip + pyparsing + python3.6 + python-dateutil + python_abi + pytz + readline + reportlab + scikit-learn + scipy + setuptools + statsmodels + tk + +[options.package_data]= + test-data=test-data/COS-3.500.fastq,test-data/COS-3.fasta,test-data/COS-3.fastq,test-data/COS-5.fasta + test-data/COS-5.fastq,test-data/DTR-long.fasta,test-data/DTR-long.fastq,test-data/DTR-short.fasta + test-data/DTR-short.fastq,test-data/Headful.fasta,test-data/Headful.fastq,test-data/Mu-like.fasta + test-data/Mu-like_R1.fastq,test-data/Mu-like_R2.fastq,test-data/Virome.fasta + test-data/Virome.fastq,test-data/chk_0_2_10_0.npz + data-virome=data-virome/Contigs_30min.fasta,data-virome/SRR4295172_2_div6.fastq,data-virome/SRR4295172_1_div6.fastq + unit-tests-data=unit-tests/data/G-janv_S2_R1_001.fastq.500,unit-tests/data/G-janv_S2_R2_001.fastq.500 + unit-tests/data/chk_0_0_38_863.npz,unit-tests/data/coverage0_0.npz,unit-tests/data/seq1_2_3.fasta + non-regression-tests-data=non-regression-tests/data/HK97_assembly.fasta,non-regression-tests/data/Lambda_assembly.fasta + non-regression-tests/data/P1_assembly.fasta,non-regression-tests/data/R1_1M_READS_EACH_PHAGE(1).fastq.4 + non-regression-tests/data/R1_1M_READS_EACH_PHAGE.fastq.20,non-regression-tests/data/R2_1M_READS_EACH_PHAGE(1).fastq.4 + non-regression-tests/data/R2_1M_READS_EACH_PHAGE.fastq.20,non-regression-tests/data/Staph1N_assembly.fasta + non-regression-tests/data/T4_assembly.fasta,non-regression-tests/data/T7_assembly.fasta + non-regression-tests/data/virome_6seq.fa diff --git a/setup.py b/setup.py new file mode 100644 index 0000000000000000000000000000000000000000..0407ad7928fd4da073f06236c39237e1abee34e6 --- /dev/null +++ b/setup.py @@ -0,0 +1,17 @@ +"""A setuptools based setup module. +See: +https://packaging.python.org/guides/distributing-packages-using-setuptools/ +https://github.com/pypa/sampleproject +""" + +# Always prefer setuptools over distutils +from setuptools import setup, find_packages +import pathlib + +here = pathlib.Path(__file__).parent.resolve() + +# Get the long description from the README file +# long_description = (here / "README.md").read_text(encoding="utf-8") +#long_description = (here / "README.txt").read_text(encoding="utf-8") + +setup() \ No newline at end of file