Fix mkdocs issues

docs/BRC4_genome_loader.md

@@ -1,9 +1,9 @@
 ## BRC4_genome_loader
-### Module: [Bio::EnsEMBL::Pipeline::PipeConfig::BRC4_genome_loader_conf](../src/perl/Bio/EnsEMBL/Pipeline/PipeConfig/BRC4_genome_loader_conf.pm)
+### Module: [Bio::EnsEMBL::Pipeline::PipeConfig::BRC4_genome_loader_conf](https://github.com/Ensembl/ensembl-genomio/blob/main/src/perl/Bio/EnsEMBL/Pipeline/PipeConfig/BRC4_genome_loader_conf.pm)
 
 Creates an [Ensembl core database](http://www.ensembl.org/info/docs/api/core/index.html)
 from a set of flat files
-or adds ad-hoc (ie organellas) sequences to the existing core.
+or adds ad-hoc (i.e. organellas) sequences to the existing core.
 
 ### Prerequisites
 A registry file with the locations of the core database server(s) and the production database (or `-production_db $PROD_DB_URL` specified).

docs/cicd_gitlab.md

@@ -1,5 +1,5 @@
 ## [Gitlab CI/CD](https://docs.gitlab.com/ee/ci/) pipelines
-### Location [gitlab/cicd](../gitlab/cicd)
+### Location [cicd/gitlab](https://github.com/Ensembl/ensembl-genomio/blob/main/cicd/gitlab)
 
 Some Gitlab based CI/CD helper pipelines
 
@@ -14,17 +14,17 @@ See this [Gitlab documentation](https://docs.gitlab.com/ee/user/project/import/g
 2) Get repo
 
 3) Create (if you need)  cicd/gitlab folders, add configs.
-We use [cicd/gitlab/dot.gitlab-ci.yml](../cicd/gitlab/dot.gitlab-ci.yml) for this repo instead the default one (see below).
+We use [cicd/gitlab/dot.gitlab-ci.yml](https://github.com/Ensembl/ensembl-genomio/blob/main/cicd/gitlab/dot.gitlab-ci.yml) for this repo instead the default one (see below).
 
 4) Edit settings for CI/CD
 [General pipelines] expand
-set "CI/CD configuration file" to [cicd/gitlab/dot.gitlab-ci.yml](../cicd/gitlab/dot.gitlab-ci.yml)
-click [Save changes] at the end of this small section
+Set "CI/CD configuration file" to [cicd/gitlab/dot.gitlab-ci.yml](https://github.com/Ensembl/ensembl-genomio/blob/main/cicd/gitlab/dot.gitlab-ci.yml)
+Click [Save changes] at the end of this small section
 
-5) enable runners
-General pipelines] expand
+5) Enable runners
+[General pipelines] expand
 [Runners] expand
-pick "Shared runners"
+Pick "Shared runners"
 
 6) Customize email settings
 Like it's stated on the [official documentation](https://docs.gitlab.com/ee/user/project/integrations/pipeline_status_emails.html):
@@ -38,7 +38,7 @@ Like it's stated on the [official documentation](https://docs.gitlab.com/ee/user
 ## A few notes on style
 
 * We suggest separating logic for running various parts into separate pipelines and using different `trigger` jobs to invoke these pipelines.
-As for now we have [cicd/gitlab/parts/](../cicd/gitlab/parts/) folder for these needs.
+As for now we have [cicd/gitlab/parts/](https://github.com/Ensembl/ensembl-genomio/blob/main/cicd/gitlab/parts/) folder for these needs.
 
 * Feel free to use external pipelines (as `trigger` jobs) or other parts from [GitLab templates](https://gitlab.com/gitlab-org/gitlab/-/tree/master/lib/gitlab/ci/templates). Though for pipelines, please, add 
 ```

docs/scripts/gen_ref_pages.py

@@ -22,47 +22,28 @@
 
 nav = mkdocs_gen_files.Nav()
 
-root = Path("src/python/ensembl/brc4")
-for py_path in sorted(root.rglob("*.py")):
-    # Drop "src/python" from the path components
-    parts = py_path.parts[2:]
-
-    if parts[-1] == "__main__.py":
-        continue
-
-    doc_path = py_path.relative_to(root).with_suffix(".md")
+root = Path("src/python").resolve()
+ensembl_path = root / "ensembl"
+for py_path in sorted(ensembl_path.rglob("*.py")):
+    # Get the relative module path and corresponding documentation paths
+    module_path = py_path.relative_to(root)
+    doc_path = module_path.with_suffix(".md")
     full_doc_path = Path("reference", doc_path)
-
-    if parts[-1] == "__init__.py":
+    # Get all the parts of the module path without the ".py" extension
+    parts = tuple(module_path.with_suffix("").parts)
+    # Drop "__init__" file from the path components as well (if present)
+    if parts[-1] == "__init__":
         parts = parts[:-1]
         doc_path = doc_path.with_name("index.md")
         full_doc_path = full_doc_path.with_name("index.md")
-
-    nav[parts] = doc_path.as_posix()
-
-    with mkdocs_gen_files.open(full_doc_path, "w") as fd:
-        identifier = ".".join(parts).replace(".py", "")
-        fd.write(f"::: {identifier}\n")
-
-    mkdocs_gen_files.set_edit_path(full_doc_path, Path("../") / py_path)
-
-root = Path("src/python/ensembl/io")
-num_parents = len(root.parents) - 2
-for init_path in sorted(root.rglob("__init__.py")):
-    # Get the relative module path
-    module_path = init_path.relative_to(root).parent
-    doc_path = module_path.with_suffix(".md")
-    full_doc_path = Path("reference", doc_path)
-    # Drop all the parents of the namespace and "__init__.py" file from the path components
-    parts = init_path.parts[num_parents:-1]
     # Add markdown file path with its index tree
     nav[parts] = doc_path.as_posix()
-    # Populate the markdown file with the doc stub of this Python module
-    with mkdocs_gen_files.open(full_doc_path, "a") as fd:
+    # Populate the markdown file with the doc stub of this module
+    with mkdocs_gen_files.open(full_doc_path, "w") as fd:
         identifier = ".".join(parts)
         fd.write(f"::: {identifier}\n")
     # Correct the path
-    mkdocs_gen_files.set_edit_path(full_doc_path, Path("../") / init_path)
+    mkdocs_gen_files.set_edit_path(full_doc_path, module_path)
 
 with mkdocs_gen_files.open("reference/summary.md", "w") as nav_file:
     nav_file.writelines(nav.build_literate_nav())

docs/trf_split_run.md

@@ -1,7 +1,7 @@
-# [trf_split_run.bash](scripts/trf_split_run.bash)
+# [trf_split_run.bash](https://github.com/Ensembl/ensembl-genomio/blob/main/scripts/trf_split_run.bash)
 
 A trf wrapper with chunking support to be used with
-[ensembl-production-imported DNAFeatures pipeline](https://github.com/Ensembl/ensembl-production-imported/tree/main/src/perl/Bio/EnsEMBL/EGPipeline/PipeConfig/DNAFeatures_conf.pm) (see [docs](docs/trf_split_run.md))
+[ensembl-production-imported DNAFeatures pipeline](https://github.com/Ensembl/ensembl-production-imported/tree/main/src/perl/Bio/EnsEMBL/EGPipeline/PipeConfig/DNAFeatures_conf.pm)
 Compatible compatible with input/output format of trf invocation from [Bio::EnsEMBL::Analysis::Runnable::TRF](https://github.com/Ensembl/ensembl-analysis/blob/main/modules/Bio/EnsEMBL/Analysis/Runnable/TRF.pm).
 And can be used as a hack to allow TRF stage to be accomplished at the cost of splitting
  long repeat into several adjacent ones  (with possible losses).
@@ -14,7 +14,7 @@ python -c 'from Bio import SeqIO' || echo "no biopython" >> /dev/stderr
 ```
 
 ## Options
-Use environment variable to control scipt run
+Use environment variable to control script run
 * `DNA_FEATURES_TRF_SPLIT_NO_SPLITTING` -- set to `YES` to skip splitting stage
 * `DNA_FEATURES_TRF_SPLIT_NO_TRF` -- set to `YES` to skip trf stage
 * `DNA_FEATURES_TRF_SPLIT_SPLITTER_CHUNK_SIZE` -- chunk size [`1_000_000`]

mkdocs.yml

@@ -33,9 +33,6 @@ theme:
     code: IBM Plex Mono
   features:
       - content.tooltips
-      - navigation.expand
-      - navigation.tabs
-      - navigation.tabs.sticky
       - navigation.top
       - search.highlight
       - search.suggest

pyproject.toml

@@ -53,7 +53,7 @@ dependencies = [
     "biopython == 1.81",
     "ensembl-hive @ git+https://github.com/Ensembl/ensembl-hive.git",
     "ensembl-py @ git+https://github.com/Ensembl/ensembl-py.git",  # minimum v2.0.0
-    "ensembl-utils >= 0.1.3",
+    "ensembl-utils >= 0.2.0",
     "jsonschema >= 4.6.0",
     "intervaltree >= 3.1.0",
     "mysql-connector-python >= 8.0.29",

src/python/ensembl/io/genomio/data/__init__.py

@@ -0,0 +1,15 @@
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Data files."""