Merge pull request #14 from draeger-lab/dev

Dev->main in preparation for release 0.0.dev1
draeger-lab · Aug 28, 2024 · 3ddc62a · 3ddc62a
2 parents ee7f65c + 5eeb0ce
commit 3ddc62a
Show file tree

Hide file tree

Showing 37 changed files with 14,969 additions and 3,269 deletions.
diff --git a/README.md b/README.md
@@ -11,27 +11,28 @@
 
 # SPECIMEN
 
-SPECIMEN is a collection of different workflows designed for the automated and standardised curation of genome-scale models. It is mainly based on the [refineGEMs toolbox](https://github.com/draeger-lab/refinegems/tree/dev-2), but also includes additional tools like [CarveMe](https://carveme.readthedocs.io/en/latest/).
+SPECIMEN is a collection of different workflows designed for the automated and standardised curation of genome-scale models. It is mainly based on the [refineGEMs toolbox](https://github.com/draeger-lab/refinegems/tree/main), but also includes additional tools like [CarveMe](https://carveme.readthedocs.io/en/latest/).
 
-> Note: This tool is currently still under active developement, any feedback or ides are welcome.
+> Note: <br> 
+  This tool is currently still under active developement, any feedback or ideas are welcome. Also, since its developemental, please note that bugs and error will probably occur. Please feel free to report them to the developers.
 
 Currently avaible workflow:
 
 - CMPB - CarveMe-ModelPolisher based:\\Starting from a CarveMe draft model, refine and extend it towards a high-quality stain-specific model
 
-    > Note: For a future update, optional direct integration of CarveMe into the pipeline is planned
-
 - HQTB - High-quality template based:\\This pipeline follows the modelling approach of using a high-quality template model as a basis for the reconstruction of a new model from a new genome (e.g. a different strain). 
 
+> Note: Due to some major refactoring changes in refineGEMs this workflow might not run as expected.
+
 - PGAB: under construction
 
 ## Installation  
 
 Download this repository and run the command `pip install -e .` inside the top-level directory.     
 
-When running the HQTB Pipeline, further tools need to be installed:
+When running certain steps, further tools need to be installed:
 
-- [DIAMOND, version 2.0.4 or higher](https://github.com/bbuchfink/diamond)
+- [DIAMOND, version 2.0.4 or higher](https://github.com/bbuchfink/diamond), needed for GeneGapFiller and HQTB
 - [EntrezDirect](https://www.ncbi.nlm.nih.gov/books/NBK179288/), if no NCBI mapping has been created beforehand
 
 ## Quickstart

diff --git a/dev/CB_test_modules.ipynb b/dev/CB_test_modules.ipynb
diff --git a/dev/README.md b/dev/README.md
@@ -0,0 +1,21 @@
+# Developer Zone
+
+This is a directory containing information, notebooks with open work and testing examples and much more for the developers of the SPECIMEN package. It also serves as an additional hub, where developers can share and discuss their code.
+
+Additionally, some helpful code for making developement easier and standardised between developers has been added here as well.
+
+More information about the different files collected here can be found below.
+
+## Working Progress Notebooks
+
+- ``test_modules``: <br>
+    Test the different workflows their substeps. <br>
+    Status: Ready to run, just adjust the parameters
+
+## Help with Coding
+
+- `docstring-format.mustache`<br>
+  As the name suggest, this file contains the basic setup for the docstring
+  format used for this package. It can be integrated into your IDE (e.g. VSCode) to allow autodoc to use the correct style.
+- `TodoTree_params.txt`<br>
+  If you use VSCode, you can install the TodoTree extension and add this file to your settings.json. It will highlight all listed keyword can collect them in a seperate tab. This makes it easier to track TODOs, points of DISCUSSIONs and more and allows faster identification of open issues inside the code.
diff --git a/dev/TodoTree_params.txt b/dev/TodoTree_params.txt
@@ -0,0 +1,88 @@
+    "todo-tree.general.statusBar": "tags",
+    "todo-tree.general.tags": [
+            "@BUG",
+            "@HACK",
+            "@FIXME",
+            "@TODO",
+            "XXX",
+            "[ ]",
+            "[x]",
+            "@TEST",
+            "@DEPRECATE",
+            "@NOTE",
+            "@DISCUSSION",
+            "@DEBUG"
+        ],
+    "todo-tree.highlights.backgroundColourScheme": [
+        "red",
+        "orange",
+        "yellow",
+        "cyan",
+        "blue",
+        "indigo",
+        "violet",
+        "#ff43a4",
+        "#c0c0c0",
+        "#f5bd02",
+        "violet",
+        "#329542"
+    ],
+    "todo-tree.highlights.foregroundColourScheme": [
+        "white",
+        "black",
+        "black",
+        "black",
+        "white",
+        "white",
+        "black",
+        "black",
+        "black",
+        "black",
+        "black",
+        "white"
+    ],
+    "todo-tree.highlights.useColourScheme": true,
+    "todo-tree.tree.showCountsInTree": true,
+    "todo-tree.general.showActivityBarBadge": true,
+    "todo-tree.general.showIconsInsteadOfTagsInStatusBar": true,
+    "todo-tree.highlights.customHighlight":{
+        "@TODO": {
+            "icon": "check-circle"
+        },
+        "@BUG": {
+            "icon": "bug"
+        },
+        "@HACK": {
+            "icon": "tools"
+        },
+        "@FIXME": {
+            "icon": "flame"
+        },
+        "XXX": {
+            "icon": "x"
+        },
+        "[ ]": {
+            "icon": "issue-draft"
+        },
+        "[x]": {
+            "icon": "issue-closed"
+        },
+        "@TEST": {
+            "icon": "beaker"
+        },
+        "@DEPRECATE": {
+            "icon": "trash"
+        },
+        "@NOTE": {
+            "icon": "note"
+        },
+        "@DISCUSSION": {
+            "icon": "comment-discussion"
+        },
+        "@DEBUG": {
+            "icon": "bug"
+        }
+    },
+    "todo-tree.general.tagGroups": {
+
+    },