Merge pull request #2 from EBI-Metagenomics/dev

fix cli path when installing with pip

Author: chrisAta

pimento.py cli/pimento.pypimento.py renamed to cli/pimento.py

@@ -1,6 +1,6 @@
 [project]
 name = "mi-pimento"
-version = "0.0.1"
+version = "0.0.2"
 readme = "README.md"
 license = {text = "Apache Software License 2.0"}
 authors = [
@@ -30,10 +30,11 @@ requires = ["setuptools>=61.0"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools]
-packages = ["bin"]
+packages = ["cli",
+            "bin"]
 
 [project.scripts]
-pimento = "pimento:cli"
+pimento = "cli.pimento:cli"
 
 [project.optional-dependencies]
 tests = [

pyproject.toml

@@ -2,21 +2,21 @@
   tags:
     - are_there_primers
   exit_code: 2
-  command: python -m pimento std --chromosome X
+  command: python -m cli.pimento std --chromosome X
   stderr:
     contains:
       - "Error: No such option: --chromosome"
 - name: are_there_primers test_correct_args
   tags:
     - are_there_primers
-  command: python -m pimento are_there_primers -i tests/fixtures/test.fastq.gz -o sample
+  command: python -m cli.pimento are_there_primers -i tests/fixtures/test.fastq.gz -o sample
   files:
     - path: "sample_general_primer_out.txt"
       md5sum: f2160c8ffedf48068f2e1137e0a3a7e7
 - name: are_there_primers test_big_file
   tags:
     - are_there_primers
-  command: python -m pimento are_there_primers -i tests/fixtures/test_big.fastq.gz -o sample
+  command: python -m cli.pimento are_there_primers -i tests/fixtures/test_big.fastq.gz -o sample
   files:
     - path: "sample_general_primer_out.txt"
       md5sum: f2160c8ffedf48068f2e1137e0a3a7e7

tests/unit/test_are_there_primers.yml

@@ -2,21 +2,21 @@
   tags:
     - choose_primer_cutoff
   exit_code: 2
-  command: python -m pimento choose_primer_cutoff --chromosome X
+  command: python -m cli.pimento choose_primer_cutoff --chromosome X
   stderr:
     contains:
       - "Error: No such option: --chromosome"
 - name: choose_primer_cutoff test_correct_args
   tags:
     - choose_primer_cutoff
-  command: python -m pimento choose_primer_cutoff -i tests/fixtures/test.fastq.gz -p tests/fixtures/test_cutoffs.tsv -o sample
+  command: python -m cli.pimento choose_primer_cutoff -i tests/fixtures/test.fastq.gz -p tests/fixtures/test_cutoffs.tsv -o sample
   files:
     - path: "sample_auto_primers.fasta"
       md5sum: c36ff305d6aec14df3b7a61cb702101e
 - name: choose_primer_cutoff test_large_file
   tags:
     - choose_primer_cutoff
-  command: python -m pimento choose_primer_cutoff -i tests/fixtures/test_big.fastq.gz -p tests/fixtures/test_cutoffs_big.tsv -o sample
+  command: python -m cli.pimento choose_primer_cutoff -i tests/fixtures/test_big.fastq.gz -p tests/fixtures/test_cutoffs_big.tsv -o sample
   files:
     - path: "sample_auto_primers.fasta"
       md5sum: b6abc080cbb4390dce82b23fc176f3c2

tests/unit/test_choose_primer_cutoff.yml

@@ -2,21 +2,21 @@
   tags:
     - find_cutoffs
   exit_code: 2
-  command: python -m pimento find_cutoffs --chromosome X
+  command: python -m cli.pimento find_cutoffs --chromosome X
   stderr:
     contains:
       - "Error: No such option: --chromosome"
 - name: find_cutoffs test_correct_args
   tags:
     - find_cutoffs
-  command: python -m pimento find_cutoffs -i tests/fixtures/test_bcv.tsv -o sample
+  command: python -m cli.pimento find_cutoffs -i tests/fixtures/test_bcv.tsv -o sample
   files:
     - path: "sample_cutoffs.tsv"
       md5sum: b4da973b056b9b5ed4ec7ca8d7998be4
 - name: find_cutoffs test_large_file
   tags:
     - find_cutoffs
-  command: python -m pimento find_cutoffs -i tests/fixtures/test_big_bcv.tsv -o sample
+  command: python -m cli.pimento find_cutoffs -i tests/fixtures/test_big_bcv.tsv -o sample
   files:
     - path: "sample_cutoffs.tsv"
       md5sum: 80767a078f817aab1b9c67736d14093b

tests/unit/test_find_cutoffs.yml

@@ -2,21 +2,21 @@
   tags:
     - generate_bcv
   exit_code: 2
-  command: python -m pimento std --chromosome X
+  command: python -m cli.pimento std --chromosome X
   stderr:
     contains:
       - "Error: No such option: --chromosome"
 - name: generate_bcv test_correct_args
   tags:
     - generate_bcv
-  command: python -m pimento gen_bcv -i tests/fixtures/test.fastq.gz -st FR -o sample
+  command: python -m cli.pimento gen_bcv -i tests/fixtures/test.fastq.gz -st FR -o sample
   files:
     - path: "sample_bcv.tsv"
       md5sum: 875c712aadf9b21bd535e555dbb4b7e1
 - name: generate_bcv test_large_file
   tags:
     - generate_bcv
-  command: python -m pimento gen_bcv -i tests/fixtures/test_big.fastq.gz -st FR -o sample
+  command: python -m cli.pimento gen_bcv -i tests/fixtures/test_big.fastq.gz -st FR -o sample
   files:
     - path: "sample_bcv.tsv"
       md5sum: e4e43a0b9eb6c1c7d1cf9f10926b24c3

tests/unit/test_generate_bcv.yml

@@ -2,21 +2,21 @@
   tags:
     - primer_cutoff_strategy
   exit_code: 2
-  command: python -m pimento choose_primer_cutoff --chromosome X
+  command: python -m cli.pimento choose_primer_cutoff --chromosome X
   stderr:
     contains:
       - "Error: No such option: --chromosome"
 - name: primer_cutoff_strategy test_correct_args
   tags:
     - primer_cutoff_strategy
-  command: python -m pimento auto -i tests/fixtures/test.fastq.gz -st FR -o sample
+  command: python -m cli.pimento auto -i tests/fixtures/test.fastq.gz -st FR -o sample
   files:
     - path: "sample_auto_primers.fasta"
       md5sum: c36ff305d6aec14df3b7a61cb702101e
 - name: primer_cutoff_strategy test_large_file
   tags:
     - primer_cutoff_strategy
-  command: python -m pimento auto -i tests/fixtures/test_big.fastq.gz -st FR -o sample
+  command: python -m cli.pimento auto -i tests/fixtures/test_big.fastq.gz -st FR -o sample
   files:
     - path: "sample_auto_primers.fasta"
       md5sum: b6abc080cbb4390dce82b23fc176f3c2

tests/unit/test_primer_cutoff_strategy.yml

@@ -2,14 +2,14 @@
   tags:
     - standard_primer_matching
   exit_code: 2
-  command: python -m pimento std --chromosome X
+  command: python -m cli.pimento std --chromosome X
   stderr:
     contains:
       - "Error: No such option: --chromosome"
 - name: standard_primer_matching test_correct_args
   tags:
     - standard_primer_matching
-  command: python -m pimento std -i tests/fixtures/test.fastq.gz -p standard_primers -o sample
+  command: python -m cli.pimento std -i tests/fixtures/test.fastq.gz -p standard_primers -o sample
   files:
     - path: "sample_std_primers.fasta"
       md5sum: f26cdc22a5231d2dbd0831f1f1983dc6