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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