From 69ce83577da7c1df83568a31d36b042422d4ca3f Mon Sep 17 00:00:00 2001
From: Veronique Legrand <vlegrand@pasteur.fr>
Date: Fri, 8 Jul 2022 18:09:08 +0200
Subject: [PATCH] work in progress for packaging and redistributing
---
setup.cfg | 62 ++++++++++++++++++++++++++++++++++++++++---------------
1 file changed, 45 insertions(+), 17 deletions(-)
diff --git a/setup.cfg b/setup.cfg
index 5ab250f..67935c0 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,6 +1,6 @@
[metadata]
name = phageTermVirome
-version = 2.0
+version = 2.1
author = Marc Monot
author_email = marc.monot@pasteur.fr
description = Using sequencing bias to identify phages terminii and phage genome packaging.
@@ -19,7 +19,13 @@ platforms=any
[options]
package_dir =
= .
-packages = find:
+ = _modules
+ = test-data
+
+[options.entry_points]
+console_script =
+ PhageTermVirome = ptv.PhageTerm:main
+
python_requires = >=3.6
[options.packages.find]
@@ -52,18 +58,40 @@ install_requires =
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
+[options.data_files]=
+ 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
--
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