update doc for bigscape (#270)

* remove blank line * add missing "#" * Update bigscape.md `run_bigscape` is already included in the `bigscape` module. * update doc about bigscape * format and update the explanation on bigscape parameters * add extra css to ensure auto-wrap in code block * Apply suggestions from code review Co-authored-by: Giulia Crocioni <[email protected]> --------- Co-authored-by: Giulia Crocioni <[email protected]>
NPLinker · Jul 29, 2024 · 7ac74fa · 7ac74fa
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diff --git a/docs/api/bigscape.md b/docs/api/bigscape.md
@@ -1,2 +1 @@
-::: nplinker.genomics.bigscape
-::: nplinker.genomics.bigscape.run_bigscape
+::: nplinker.genomics.bigscape
diff --git a/docs/concepts/bigscape.md b/docs/concepts/bigscape.md
@@ -1,19 +1,6 @@
 NPLinker can run BigScape automatically if the `bigscape` directory does not exist in the working directory.
+Both version 1 and version 2 of BigScape are supported.
 
-To run BigScape, NPLinker requires the following BigScape parameters:
+See the [configuration template][configuration-template] for how to set parameters for running BigScape.
 
-- `--mix`
-- `--include_singletons`
-- `--cutoffs`
-
-And the following parameters are not allowed:
-
-- `--inputdir`
-- `--outputdir`
-- `--pfam_dir`
-
-If BigScape parameter `--mibig` is set, make sure setting the  `mibig.to_use` to true in your config file `nplinker.toml` and `mibig.version` to the version of mibig used by bigscape.
-
-
-See the [default configurations](./config_file.md#default-configurations) for the default 
-parameters of BigScape.
+See the [default configurations][default-configurations] for the default parameters used in NPLinker.
diff --git a/docs/css/extra.css b/docs/css/extra.css
@@ -0,0 +1,4 @@
+pre code {
+    white-space: pre-wrap;
+    word-wrap: break-word;
+}
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -44,6 +44,9 @@ extra:
   version:
     provider: mike
 
+extra_css:
+  - css/extra.css
+
 # https://www.mkdocs.org/user-guide/configuration/#validation
 validation:
   omitted_files: warn

diff --git a/src/nplinker/data/nplinker.toml b/src/nplinker/data/nplinker.toml
@@ -46,19 +46,23 @@ version = "3.1"
 # Version of BiG-SCAPE to run. Make sure to change the parameters property below as well
 # when changing versions.
 version = 1
-# Required bigscape parameters are `--mix`, `--include_singletons` and `--cutoffs`. NPLinker needs
-# them to run the analysis properly.
-# Parameters that must NOT exist: `--inputdir`, `--outputdir`, `--pfam_dir`. NPLinker will
-# automatically configure them.
-# If parameter `--mibig` is set, make sure setting the config `mibig.to_use` to true and
-# `mibig.version` to the version of mibig in bigscape.
+# Required BiG-SCAPE parameters.
+# --------------
+# For version 1:
+# -------------
+# Required parameters are: `--mix`, `--include_singletons` and `--cutoffs`. NPLinker needs them to run the analysis properly.
+# Do NOT set these parameters: `--inputdir`, `--outputdir`, `--pfam_dir`. NPLinker will automatically configure them.
+# If parameter `--mibig` is set, make sure to set the config `mibig.to_use` to true and `mibig.version` to the version of mibig in BiG-SCAPE.
 # The default value is "--mibig --clans-off --mix --include_singletons --cutoffs 0.30".
+# --------------
+# For version 2:
+# --------------
+# Note that BiG-SCAPE v2 has subcommands. NPLinker requires the `cluster` subcommand and its parameters.
+# Required parameters of `cluster` subcommand are: `--mibig_version`, `--include_singletons` and `--gcf_cutoffs`.
+# DO NOT set these parameters: `--pfam_path`, `--inputdir`, `--outputdir`. NPLinker will automatically configure them.
+# BiG-SCPAPE v2 also runs a `--mix` analysis by default, so you don't need to set this parameter here.
+# Example parameters for BiG-SCAPE v2: "--mibig_version 3.1 --include_singletons --gcf_cutoffs 0.30"
 parameters = "--mibig --clans-off --mix --include_singletons --cutoffs 0.30"
-# for version 2, use the following parameters string:
-# parameters = "--mibig_version 3.1 --include_singletons --gcf_cutoffs 0.30"
-# Note that BiG-SCAPE v2 has subcommands. NPLinker requires the "cluster" subcommand and its parameters to be used. 
-NPLinker will automatically set the following parameters: `--pfam_path`, `--inputdir` and `--outputdir`. So, do not set them here.
-# BiG-SCPAPE v2 also runs a --mix analysis by default, and does not need this to be included.
 # Which bigscape cutoff to use for NPLinker analysis.
 # There might be multiple cutoffs in bigscape output.
 # Note that this value must be a string.

diff --git a/src/nplinker/nplinker_default.toml b/src/nplinker/nplinker_default.toml
@@ -11,7 +11,6 @@ version = "3.1"
 [bigscape]
 version = 1
 parameters = "--mibig --clans-off --mix --include_singletons --cutoffs 0.30"
-
 cutoff = "0.30"
 
 [scoring]