Add pygenomeviz as dev deps

pyproject.toml

@@ -46,6 +46,8 @@ dev-dependencies = [
     "mkdocs-jupyter>=0.21.0",
     "mkdocs-material>=8.2",
     "black>=22.3.0",
+    # additional
+    "pygenomeviz>=1.5.0",
 ]
 
 [tool.pytest.ini_options]

requirements-dev.lock

@@ -4,15 +4,15 @@
 # last locked with the following flags:
 #   pre: false
 #   features: []
-#   all-features: false
+#   all-features: true
 #   with-sources: false
 #   generate-hashes: false
 #   universal: false
 
 -e file:.
-asttokens==2.4.1
+asttokens==3.0.0
     # via stack-data
-attrs==24.2.0
+attrs==24.3.0
     # via jsonschema
     # via referencing
 babel==2.16.0
@@ -21,14 +21,15 @@ beautifulsoup4==4.12.3
     # via nbconvert
 biopython==1.84
     # via pycirclize
-black==24.8.0
-bleach==6.1.0
+    # via pygenomeviz
+black==24.10.0
+bleach==6.2.0
     # via nbconvert
-certifi==2024.8.30
+certifi==2024.12.14
     # via requests
 cfgv==3.4.0
     # via pre-commit
-charset-normalizer==3.3.2
+charset-normalizer==3.4.0
     # via requests
 click==8.1.7
     # via black
@@ -41,38 +42,38 @@ comm==0.2.2
     # via ipykernel
 contourpy==1.3.0
     # via matplotlib
-coverage==7.6.1
+coverage==7.6.9
     # via pytest-cov
 cycler==0.12.1
     # via matplotlib
-debugpy==1.8.5
+debugpy==1.8.11
     # via ipykernel
 decorator==5.1.1
     # via ipython
 defusedxml==0.7.1
     # via nbconvert
-distlib==0.3.8
+distlib==0.3.9
     # via virtualenv
 exceptiongroup==1.2.2
     # via ipython
     # via pytest
 executing==2.1.0
     # via stack-data
-fastjsonschema==2.20.0
+fastjsonschema==2.21.1
     # via nbformat
-filelock==3.16.0
+filelock==3.16.1
     # via virtualenv
-fonttools==4.53.1
+fonttools==4.55.3
     # via matplotlib
 ghp-import==2.1.0
     # via mkdocs
-griffe==1.3.0
+griffe==1.5.1
     # via mkdocstrings-python
-identify==2.6.0
+identify==2.6.3
     # via pre-commit
-idna==3.8
+idna==3.10
     # via requests
-importlib-metadata==8.4.0
+importlib-metadata==8.5.0
     # via jupyter-client
     # via markdown
     # via mkdocs
@@ -87,7 +88,7 @@ ipykernel==6.29.5
     # via mkdocs-jupyter
 ipython==8.18.1
     # via ipykernel
-jedi==0.19.1
+jedi==0.19.2
     # via ipython
 jinja2==3.1.4
     # via mkdocs
@@ -96,9 +97,9 @@ jinja2==3.1.4
     # via nbconvert
 jsonschema==4.23.0
     # via nbformat
-jsonschema-specifications==2023.12.1
+jsonschema-specifications==2024.10.1
     # via jsonschema
-jupyter-client==8.6.2
+jupyter-client==8.6.3
     # via ipykernel
     # via nbclient
 jupyter-core==5.7.2
@@ -109,7 +110,7 @@ jupyter-core==5.7.2
     # via nbformat
 jupyterlab-pygments==0.3.0
     # via nbconvert
-jupytext==1.16.4
+jupytext==1.16.6
     # via mkdocs-jupyter
 kiwisolver==1.4.7
     # via matplotlib
@@ -122,14 +123,15 @@ markdown==3.7
 markdown-it-py==3.0.0
     # via jupytext
     # via mdit-py-plugins
-markupsafe==2.1.5
+markupsafe==3.0.2
     # via jinja2
     # via mkdocs
     # via mkdocs-autorefs
     # via mkdocstrings
     # via nbconvert
-matplotlib==3.9.2
+matplotlib==3.9.4
     # via pycirclize
+    # via pygenomeviz
 matplotlib-inline==0.1.7
     # via ipykernel
     # via ipython
@@ -152,18 +154,18 @@ mkdocs-autorefs==1.2.0
     # via mkdocstrings-python
 mkdocs-get-deps==0.2.0
     # via mkdocs
-mkdocs-jupyter==0.25.0
-mkdocs-material==9.5.34
+mkdocs-jupyter==0.25.1
+mkdocs-material==9.5.49
     # via mkdocs-jupyter
 mkdocs-material-extensions==1.3.1
     # via mkdocs-material
-mkdocstrings==0.26.1
+mkdocstrings==0.27.0
     # via mkdocstrings-python
-mkdocstrings-python==1.11.1
+mkdocstrings-python==1.12.2
     # via mkdocstrings
 mypy-extensions==1.0.0
     # via black
-nbclient==0.10.0
+nbclient==0.10.2
     # via nbconvert
 nbconvert==7.16.4
     # via mkdocs-jupyter
@@ -181,7 +183,8 @@ numpy==2.0.2
     # via matplotlib
     # via pandas
     # via pycirclize
-packaging==24.1
+    # via pygenomeviz
+packaging==24.2
     # via black
     # via ipykernel
     # via jupytext
@@ -191,7 +194,7 @@ packaging==24.1
     # via pytest
 paginate==0.5.7
     # via mkdocs-material
-pandas==2.2.2
+pandas==2.2.3
     # via pycirclize
 pandocfilters==1.5.1
     # via nbconvert
@@ -202,44 +205,45 @@ pathspec==0.12.1
     # via mkdocs
 pexpect==4.9.0
     # via ipython
-pillow==10.4.0
+pillow==11.0.0
     # via matplotlib
-platformdirs==4.3.2
+platformdirs==4.3.6
     # via black
     # via jupyter-core
     # via mkdocs-get-deps
     # via mkdocstrings
     # via virtualenv
 pluggy==1.5.0
     # via pytest
-pre-commit==3.8.0
-prompt-toolkit==3.0.47
+pre-commit==4.0.1
+prompt-toolkit==3.0.48
     # via ipython
-psutil==6.0.0
+psutil==6.1.1
     # via ipykernel
 ptyprocess==0.7.0
     # via pexpect
 pure-eval==0.2.3
     # via stack-data
+pygenomeviz==1.5.0
 pygments==2.18.0
     # via ipython
     # via mkdocs-jupyter
     # via mkdocs-material
     # via nbconvert
-pymdown-extensions==10.9
+pymdown-extensions==10.12
     # via mkdocs-material
     # via mkdocstrings
-pyparsing==3.1.4
+pyparsing==3.2.0
     # via matplotlib
-pytest==8.3.3
+pytest==8.3.4
     # via pytest-cov
-pytest-cov==5.0.0
+pytest-cov==6.0.0
 python-dateutil==2.9.0.post0
     # via ghp-import
     # via jupyter-client
     # via matplotlib
     # via pandas
-pytz==2024.1
+pytz==2024.2
     # via pandas
 pyyaml==6.0.2
     # via jupytext
@@ -256,30 +260,28 @@ pyzmq==26.2.0
 referencing==0.35.1
     # via jsonschema
     # via jsonschema-specifications
-regex==2024.7.24
+regex==2024.11.6
     # via mkdocs-material
 requests==2.32.3
     # via mkdocs-material
-rpds-py==0.20.0
+rpds-py==0.22.3
     # via jsonschema
     # via referencing
-ruff==0.6.4
-six==1.16.0
-    # via asttokens
-    # via bleach
+ruff==0.8.4
+six==1.17.0
     # via python-dateutil
 soupsieve==2.6
     # via beautifulsoup4
 stack-data==0.6.3
     # via ipython
-tinycss2==1.3.0
+tinycss2==1.4.0
     # via nbconvert
-tomli==2.0.1
+tomli==2.2.1
     # via black
     # via coverage
     # via jupytext
     # via pytest
-tornado==6.4.1
+tornado==6.4.2
     # via ipykernel
     # via jupyter-client
 traitlets==5.14.3
@@ -296,19 +298,19 @@ typing-extensions==4.12.2
     # via black
     # via ipython
     # via mkdocstrings
-tzdata==2024.1
+tzdata==2024.2
     # via pandas
-urllib3==2.2.2
+urllib3==2.2.3
     # via requests
-virtualenv==20.26.4
+virtualenv==20.28.0
     # via pre-commit
-watchdog==5.0.2
+watchdog==6.0.0
     # via mkdocs
 wcwidth==0.2.13
     # via prompt-toolkit
 webencodings==0.5.1
     # via bleach
     # via tinycss2
-zipp==3.20.1
+zipp==3.21.0
     # via importlib-metadata
     # via importlib-resources

requirements.lock

@@ -4,7 +4,7 @@
 # last locked with the following flags:
 #   pre: false
 #   features: []
-#   all-features: false
+#   all-features: true
 #   with-sources: false
 #   generate-hashes: false
 #   universal: false
@@ -16,36 +16,36 @@ contourpy==1.3.0
     # via matplotlib
 cycler==0.12.1
     # via matplotlib
-fonttools==4.53.1
+fonttools==4.55.3
     # via matplotlib
 importlib-resources==6.4.5
     # via matplotlib
 kiwisolver==1.4.7
     # via matplotlib
-matplotlib==3.9.2
+matplotlib==3.9.4
     # via pycirclize
 numpy==2.0.2
     # via biopython
     # via contourpy
     # via matplotlib
     # via pandas
     # via pycirclize
-packaging==24.1
+packaging==24.2
     # via matplotlib
-pandas==2.2.2
+pandas==2.2.3
     # via pycirclize
-pillow==10.4.0
+pillow==11.0.0
     # via matplotlib
-pyparsing==3.1.4
+pyparsing==3.2.0
     # via matplotlib
 python-dateutil==2.9.0.post0
     # via matplotlib
     # via pandas
-pytz==2024.1
+pytz==2024.2
     # via pandas
-six==1.16.0
+six==1.17.0
     # via python-dateutil
-tzdata==2024.1
+tzdata==2024.2
     # via pandas
-zipp==3.20.1
+zipp==3.21.0
     # via importlib-resources