mgnify-pipelines-toolkit 0.0.5__py3-none-any.whl → 0.0.6__py3-none-any.whl

{mgnify_pipelines_toolkit-0.0.5.dist-info → mgnify_pipelines_toolkit-0.0.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
-Name: mgnify-pipelines-toolkit
-Version: 0.0.5
+Name: mgnify_pipelines_toolkit
+Version: 0.0.6
 Summary: Collection of scripts and tools for MGnify pipelines
 Author-email: MGnify team <metagenomics-help@ebi.ac.uk>
 License: Apache Software License 2.0
@@ -50,14 +50,14 @@ Then this command will upload it to Test-PyPi (you will need to generate an API
 
 To upload it to actual PyPi:
 
-`python3 -m twine upload dist/*`
+`python3 -m twine upload dist/mgnify_pipelines_toolkit-0.0.x*`
 
 ## Adding a new script to the package
 
 ### New script requirements
 
 There are a few requirements for your script:
-- It needs to have a named main function of some kind. See `mgnify_pipelines_toolkit/v6/get_subunits.py` and the `main()` function for an example
+- It needs to have a named main function of some kind. See `mgnify_pipelines_toolkit/analysis/shared/get_subunits.py` and the `main()` function for an example
 - Because this package is meant to be run from the command-line, make sure your script can easily pass arguments using tools like `argparse` or `click`
 - A small amount of dependencies. This requirement is subjective, but for example if your script only requires a handful of basic packages like `Biopython`, `numpy`, `pandas`, etc., then it's fine. However if the script has a more extensive list of dependencies, a container is probably a better fit.
 
@@ -65,19 +65,21 @@ There are a few requirements for your script:
 
 To add a new Python script, first copy it over to the `mgnify_pipelines_toolkit` directory in this repository, specifically to the subdirectory that makes the most sense. If none of the subdirectories make sense for your script, create a new one. If your script doesn't have a `main()` type function yet, write one. 
 
-Then, open `pyproject.toml` as you will need to add some bits. First, any dependencies required (include the version) to the `dependencies` field.
+Then, open `pyproject.toml` as you will need to add some bits. First, add any missing dependencies (include the version) to the `dependencies` field.
+
+Then, if you created a new subdirectory to add your script in, go to the `packages` line under `[tool.setuptools]` and add the new subdirectory following the same syntax.
 
 Then, scroll down to the `[project.scripts]` line. Here, you will create an alias command for running your script from the command-line. In the example line:
 
-`get_subunits = "mgnify_pipelines_toolkit.v6.get_subunits:main"`
+`get_subunits = "mgnify_pipelines_toolkit.analysis.shared.get_subunits:main"`
 
 - `get_subunits` is the alias
-- `mgnify_pipelines_toolkit.v6.get_subunits` will link the alias to the script with the path `mgnify_pipelines_toolkit/v6/get_subunits.py`
+- `mgnify_pipelines_toolkit.analysis.shared.get_subunits` will link the alias to the script with the path `mgnify_pipelines_toolkit/analysis/shared/get_subunits.py`
 - `:main` will specifically call the function named `main()` when the alias is run. 
 
 When you have setup this command, executing `get_subunits` on the command-line will be the equivalent of doing:
 
-`from mgnify_pipelines_toolkit.v6.get_subunits import main; main()`
+`from mgnify_pipelines_toolkit.analysis.shared.get_subunits import main; main()`
 
 Finally, you will need to bump up the version in the `version` line. How/when we bump versions is to be determined.
 

mgnify_pipelines_toolkit-0.0.6.dist-info/RECORD

@@ -0,0 +1,21 @@
+mgnify_pipelines_toolkit/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+mgnify_pipelines_toolkit/analysis/amplicon/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+mgnify_pipelines_toolkit/analysis/amplicon/are_there_primers.py,sha256=8w9YrRS0dKfgJPK7NlOmwOio2KKIeGzSCaqWlJlYmAY,4459
+mgnify_pipelines_toolkit/analysis/amplicon/assess_inflection_point_mcp.py,sha256=LlriVhzuDavTDHgUnInFlzzvdubtCKC6HynxEfzK-pg,6192
+mgnify_pipelines_toolkit/analysis/amplicon/assess_mcp_proportions.py,sha256=ixvutBg0W1FokLhAOOJvhdCZFeY2N605gsrKkXfn0zs,5435
+mgnify_pipelines_toolkit/analysis/amplicon/classify_var_regions.py,sha256=aLXhWjbVwJrasIbtg0hL9EeeZX5HBGkC442quYNxh0k,18297
+mgnify_pipelines_toolkit/analysis/amplicon/find_mcp_inflection_points.py,sha256=C4ZragSYWH6rd7xdcMYI461yOV1Z2z7UZGcJ-_oYJio,2891
+mgnify_pipelines_toolkit/analysis/amplicon/make_asv_count_table.py,sha256=nwRvYp_l9cS8i4l82WY5WdAWeYR-HXRmB4oJ8wsaxkA,7630
+mgnify_pipelines_toolkit/analysis/amplicon/remove_ambiguous_reads.py,sha256=IzNM4SpKoPd_sdpO_8pAvO-WGb9hOPtDH49jnlA5O8I,2174
+mgnify_pipelines_toolkit/analysis/amplicon/rev_comp_se_primers.py,sha256=EtwbB3BPz4OKVUzgfJbVEf2a9uG-Vgpl9lceQEHun7Y,1083
+mgnify_pipelines_toolkit/analysis/amplicon/standard_primer_agrep.py,sha256=wleamlGGdsWy9eddpxAVzcXYz52hdpLXlPrPoL3i934,10279
+mgnify_pipelines_toolkit/analysis/shared/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+mgnify_pipelines_toolkit/analysis/shared/get_subunits.py,sha256=93YYL9gD7yGKsirWVWMWXbnM1ukKwvZfDxLX9L5L23Q,3907
+mgnify_pipelines_toolkit/analysis/shared/get_subunits_coords.py,sha256=Y4OWjGj0C3R1D4xYSOWfE8Jlp5JYHzpxbPatqdElWo8,1241
+mgnify_pipelines_toolkit/analysis/shared/mapseq2biom.py,sha256=qm8WGdyzshKVGTyEblMnELcO0UOaL-eI-px8Or61cPM,4911
+mgnify_pipelines_toolkit-0.0.6.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+mgnify_pipelines_toolkit-0.0.6.dist-info/METADATA,sha256=6sC7zwsbk2rJC3k0JY6_c1YthuNyvmK0lHGIfdi3Dzo,4403
+mgnify_pipelines_toolkit-0.0.6.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+mgnify_pipelines_toolkit-0.0.6.dist-info/entry_points.txt,sha256=7X3ACUcOZBNpAuFchzblpjv7vz7rsaruUGuZKjj6UfM,1108
+mgnify_pipelines_toolkit-0.0.6.dist-info/top_level.txt,sha256=xA_wC7C01V3VwuDnqwRM2QYeJJ45WtvF6LVav4tYxuE,25
+mgnify_pipelines_toolkit-0.0.6.dist-info/RECORD,,

{mgnify_pipelines_toolkit-0.0.5.dist-info → mgnify_pipelines_toolkit-0.0.6.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.3)
+Generator: bdist_wheel (0.42.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

mgnify_pipelines_toolkit-0.0.6.dist-info/entry_points.txt

@@ -0,0 +1,13 @@
+[console_scripts]
+are_there_primers = mgnify_pipelines_toolkit.analysis.amplicon.are_there_primers:main
+assess_inflection_point_mcp = mgnify_pipelines_toolkit.analysis.amplicon.assess_inflection_point_mcp:main
+assess_mcp_proportions = mgnify_pipelines_toolkit.analysis.amplicon.assess_mcp_proportions:main
+classify_var_regions = mgnify_pipelines_toolkit.analysis.amplicon.classify_var_regions:main
+find_mcp_inflection_points = mgnify_pipelines_toolkit.analysis.amplicon.find_mcp_inflection_points:main
+get_subunits = mgnify_pipelines_toolkit.analysis.shared.get_subunits:main
+get_subunits_coords = mgnify_pipelines_toolkit.analysis.shared.get_subunits_coords:main
+make_asv_count_table = mgnify_pipelines_toolkit.analysis.amplicon.make_asv_count_table:main
+mapseq2biom = mgnify_pipelines_toolkit.analysis.shared.mapseq2biom:main
+remove_ambiguous_reads = mgnify_pipelines_toolkit.analysis.amplicon.remove_ambiguous_reads:main
+rev_comp_se_primers = mgnify_pipelines_toolkit.analysis.amplicon.rev_comp_se_primers:main
+standard_primer_agrep = mgnify_pipelines_toolkit.analysis.amplicon.standard_primer_agrep:main

mgnify_pipelines_toolkit-0.0.5.dist-info/RECORD

@@ -1,21 +0,0 @@
-mgnify_pipelines_toolkit/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-mgnify_pipelines_toolkit/v6/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-mgnify_pipelines_toolkit/v6/get_subunits.py,sha256=93YYL9gD7yGKsirWVWMWXbnM1ukKwvZfDxLX9L5L23Q,3907
-mgnify_pipelines_toolkit/v6/get_subunits_coords.py,sha256=Y4OWjGj0C3R1D4xYSOWfE8Jlp5JYHzpxbPatqdElWo8,1241
-mgnify_pipelines_toolkit/v6/mapseq2biom.py,sha256=qm8WGdyzshKVGTyEblMnELcO0UOaL-eI-px8Or61cPM,4911
-mgnify_pipelines_toolkit/v6/v6_amplicon/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-mgnify_pipelines_toolkit/v6/v6_amplicon/are_there_primers.py,sha256=8w9YrRS0dKfgJPK7NlOmwOio2KKIeGzSCaqWlJlYmAY,4459
-mgnify_pipelines_toolkit/v6/v6_amplicon/assess_inflection_point_mcp.py,sha256=LlriVhzuDavTDHgUnInFlzzvdubtCKC6HynxEfzK-pg,6192
-mgnify_pipelines_toolkit/v6/v6_amplicon/assess_mcp_proportions.py,sha256=ixvutBg0W1FokLhAOOJvhdCZFeY2N605gsrKkXfn0zs,5435
-mgnify_pipelines_toolkit/v6/v6_amplicon/classify_var_regions.py,sha256=aLXhWjbVwJrasIbtg0hL9EeeZX5HBGkC442quYNxh0k,18297
-mgnify_pipelines_toolkit/v6/v6_amplicon/find_mcp_inflection_points.py,sha256=C4ZragSYWH6rd7xdcMYI461yOV1Z2z7UZGcJ-_oYJio,2891
-mgnify_pipelines_toolkit/v6/v6_amplicon/make_asv_count_table.py,sha256=nwRvYp_l9cS8i4l82WY5WdAWeYR-HXRmB4oJ8wsaxkA,7630
-mgnify_pipelines_toolkit/v6/v6_amplicon/remove_ambiguous_reads.py,sha256=IzNM4SpKoPd_sdpO_8pAvO-WGb9hOPtDH49jnlA5O8I,2174
-mgnify_pipelines_toolkit/v6/v6_amplicon/rev_comp_se_primers.py,sha256=EtwbB3BPz4OKVUzgfJbVEf2a9uG-Vgpl9lceQEHun7Y,1083
-mgnify_pipelines_toolkit/v6/v6_amplicon/standard_primer_agrep.py,sha256=wleamlGGdsWy9eddpxAVzcXYz52hdpLXlPrPoL3i934,10279
-mgnify_pipelines_toolkit-0.0.5.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-mgnify_pipelines_toolkit-0.0.5.dist-info/METADATA,sha256=aqmgib6aJC5ixaQIVhWndmTxGwS3qA4ZtYUELrCOq50,4133
-mgnify_pipelines_toolkit-0.0.5.dist-info/WHEEL,sha256=Xo9-1PvkuimrydujYJAjF7pCkriuXBpUPEjma1nZyJ0,92
-mgnify_pipelines_toolkit-0.0.5.dist-info/entry_points.txt,sha256=T2a1gbjOJuvynZ5iNMZb_-ovUBa1YHe8WJo2VqEfJPQ,1042
-mgnify_pipelines_toolkit-0.0.5.dist-info/top_level.txt,sha256=xA_wC7C01V3VwuDnqwRM2QYeJJ45WtvF6LVav4tYxuE,25
-mgnify_pipelines_toolkit-0.0.5.dist-info/RECORD,,

mgnify_pipelines_toolkit-0.0.5.dist-info/entry_points.txt

@@ -1,13 +0,0 @@
-[console_scripts]
-are_there_primers = mgnify_pipelines_toolkit.v6.v6_amplicon.are_there_primers:main
-assess_inflection_point_mcp = mgnify_pipelines_toolkit.v6.v6_amplicon.assess_inflection_point_mcp:main
-assess_mcp_proportions = mgnify_pipelines_toolkit.v6.v6_amplicon.assess_mcp_proportions:main
-classify_var_regions = mgnify_pipelines_toolkit.v6.v6_amplicon.classify_var_regions:main
-find_mcp_inflection_points = mgnify_pipelines_toolkit.v6.v6_amplicon.find_mcp_inflection_points:main
-get_subunits = mgnify_pipelines_toolkit.v6.get_subunits:main
-get_subunits_coords = mgnify_pipelines_toolkit.v6.get_subunits_coords:main
-make_asv_count_table = mgnify_pipelines_toolkit.v6.v6_amplicon.make_asv_count_table:main
-mapseq2biom = mgnify_pipelines_toolkit.v6.mapseq2biom:main
-remove_ambiguous_reads = mgnify_pipelines_toolkit.v6.v6_amplicon.remove_ambiguous_reads:main
-rev_comp_se_primers = mgnify_pipelines_toolkit.v6.v6_amplicon.rev_comp_se_primers:main
-standard_primer_agrep = mgnify_pipelines_toolkit.v6.v6_amplicon.standard_primer_agrep:main