moducomp 0.7.7__tar.gz → 0.7.9__tar.gz

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Files changed (13) hide show
  1. {moducomp-0.7.7 → moducomp-0.7.9}/PKG-INFO +5 -3
  2. {moducomp-0.7.7 → moducomp-0.7.9}/README.md +4 -2
  3. {moducomp-0.7.7 → moducomp-0.7.9}/moducomp/__init__.py +1 -1
  4. {moducomp-0.7.7 → moducomp-0.7.9}/moducomp/moducomp.py +432 -269
  5. {moducomp-0.7.7 → moducomp-0.7.9}/recipe.yaml +2 -2
  6. {moducomp-0.7.7 → moducomp-0.7.9}/.gitignore +0 -0
  7. {moducomp-0.7.7 → moducomp-0.7.9}/LICENSE.txt +0 -0
  8. {moducomp-0.7.7 → moducomp-0.7.9}/moducomp/__main__.py +0 -0
  9. {moducomp-0.7.7 → moducomp-0.7.9}/moducomp/data/test_genomes/IMG2562617132.faa +0 -0
  10. {moducomp-0.7.7 → moducomp-0.7.9}/moducomp/data/test_genomes/IMG2568526683.faa +0 -0
  11. {moducomp-0.7.7 → moducomp-0.7.9}/moducomp/data/test_genomes/IMG2740892217.faa +0 -0
  12. {moducomp-0.7.7 → moducomp-0.7.9}/pixi.lock +0 -0
  13. {moducomp-0.7.7 → moducomp-0.7.9}/pyproject.toml +0 -0
{moducomp-0.7.7 → moducomp-0.7.9}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: moducomp
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- Version: 0.7.7
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+ Version: 0.7.9
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  Summary: moducomp: metabolic module completeness and complementarity for microbiomes.
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  Keywords: bioinformatics,microbiome,metabolic,kegg,genomics
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  Author-email: "Juan C. Villada" <jvillada@lbl.gov>
@@ -77,6 +77,8 @@ Small test data sets ship with `moducomp`. After installation you can confirm th
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  moducomp test --ncpus 16 --calculate-complementarity 2 --eggnog-data-dir "$EGGNOG_DATA_DIR"
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  ```
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+ The test command runs in low-memory mode by default. If you have plenty of RAM and want full-memory mode, add `--fullmem` (or `--full-mem`).
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  ### Developer install (Pixi)
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  If you want to download the code and develop locally:
@@ -125,7 +127,7 @@ You should see the command line help without errors.
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  ### ⚠️ Important note 2
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- `moducomp` is specifically designed for large scale analysis of microbiomes with hundreds of members, and works on Linux systems with at least **64GB of RAM**. Nevertheless, it can be run on **smaller systems with less RAM, using the flag `--lowmem` when running the `pipeline` command**.
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+ `moducomp` is specifically designed for large scale analysis of microbiomes with hundreds of members, and works on Linux systems with at least **64GB of RAM**. Nevertheless, it can be run on **smaller systems with less RAM, using the flag `--lowmem` (`--low-mem`) when running the `pipeline` command**. The `test` command uses low-memory mode by default and can be switched to full memory with `--fullmem` (`--full-mem`).
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  ### Notes on bundled test data
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@@ -162,7 +164,7 @@ moducomp pipeline \
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  --ncpus <number_of_cpus_to_use> \
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  --calculate-complementarity <N> # 0 to disable, 2 for 2-member, 3 for 3-member complementarity.
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  # Optional flags:
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- # --lowmem # Optional: Use this if you have less than 64GB of RAM
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+ # --lowmem/--fullmem # Optional: Use low-mem if you have less than 64GB of RAM (default is full mem)
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  # --adapt-headers # If your FASTA headers need modification
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  # --del-tmp # To delete temporary files
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  # --eggnog-data-dir /path # If EGGNOG_DATA_DIR is not set
{moducomp-0.7.7 → moducomp-0.7.9}/README.md RENAMED
@@ -52,6 +52,8 @@ Small test data sets ship with `moducomp`. After installation you can confirm th
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  moducomp test --ncpus 16 --calculate-complementarity 2 --eggnog-data-dir "$EGGNOG_DATA_DIR"
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  ```
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+ The test command runs in low-memory mode by default. If you have plenty of RAM and want full-memory mode, add `--fullmem` (or `--full-mem`).
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  ### Developer install (Pixi)
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  If you want to download the code and develop locally:
@@ -100,7 +102,7 @@ You should see the command line help without errors.
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  ### ⚠️ Important note 2
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- `moducomp` is specifically designed for large scale analysis of microbiomes with hundreds of members, and works on Linux systems with at least **64GB of RAM**. Nevertheless, it can be run on **smaller systems with less RAM, using the flag `--lowmem` when running the `pipeline` command**.
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+ `moducomp` is specifically designed for large scale analysis of microbiomes with hundreds of members, and works on Linux systems with at least **64GB of RAM**. Nevertheless, it can be run on **smaller systems with less RAM, using the flag `--lowmem` (`--low-mem`) when running the `pipeline` command**. The `test` command uses low-memory mode by default and can be switched to full memory with `--fullmem` (`--full-mem`).
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  ### Notes on bundled test data
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@@ -137,7 +139,7 @@ moducomp pipeline \
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  --ncpus <number_of_cpus_to_use> \
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  --calculate-complementarity <N> # 0 to disable, 2 for 2-member, 3 for 3-member complementarity.
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  # Optional flags:
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- # --lowmem # Optional: Use this if you have less than 64GB of RAM
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+ # --lowmem/--fullmem # Optional: Use low-mem if you have less than 64GB of RAM (default is full mem)
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  # --adapt-headers # If your FASTA headers need modification
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  # --del-tmp # To delete temporary files
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  # --eggnog-data-dir /path # If EGGNOG_DATA_DIR is not set
{moducomp-0.7.7 → moducomp-0.7.9}/moducomp/__init__.py RENAMED
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  moducomp: metabolic module completeness and complementarity for microbiomes.
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  """
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- __version__ = "0.7.7"
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+ __version__ = "0.7.9"
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  __author__ = "Juan C. Villada"
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  __email__ = "jvillada@lbl.gov"
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  __title__ = "moducomp"