diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..997504b --- /dev/null +++ b/.gitattributes @@ -0,0 +1,2 @@ +# SCM syntax highlighting & preventing 3-way merges +pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index f7fddfc..7f5a621 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -6,8 +6,6 @@ on: pull_request: branches: - "*" - schedule: - - cron: "0 19 * * SUN" jobs: @@ -38,7 +36,7 @@ jobs: run: pre-commit run --all-files - name: Run tests - run: pytest tests --doctest-modules --cov=dram_viz --cov-report=xml --cov-report=html + run: python -m pytest tests --doctest-modules --cov=dram_viz --cov-report=xml --cov-report=html - name: Upload coverage to Codecov uses: codecov/codecov-action@v3 diff --git a/.gitignore b/.gitignore index 9c2aef9..3947bc2 100644 --- a/.gitignore +++ b/.gitignore @@ -81,3 +81,6 @@ __pycache__/ ## File-based project format: *.iws +# pixi environments +.pixi/* +!.pixi/config.toml diff --git a/dram_viz/rule_parser/.github/workflows/python-test.yml b/dram_viz/rule_parser/.github/workflows/python-test.yml deleted file mode 100644 index adddd45..0000000 --- a/dram_viz/rule_parser/.github/workflows/python-test.yml +++ /dev/null @@ -1,36 +0,0 @@ -# This workflow will install Python dependencies, run tests and lint with a single version of Python -# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python - -name: Test - -on: - push: - branches: ["main"] - pull_request: - branches: ["main"] - -permissions: - contents: read - -jobs: - build: - runs-on: ubuntu-latest - - steps: - - uses: actions/checkout@v4 - - name: Set up Python 3.12 - uses: actions/setup-python@v3 - with: - python-version: "3.12" - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install pre-commit pytest - if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - - name: Install pre-commit hooks - run: pre-commit install - - name: Run pre-commit hooks for linting and other checks - run: pre-commit run --all-files - - name: Test with pytest - run: | - python -m pytest tests diff --git a/dram_viz/rule_parser/.gitignore b/dram_viz/rule_parser/.gitignore deleted file mode 100644 index f18571f..0000000 --- a/dram_viz/rule_parser/.gitignore +++ /dev/null @@ -1,207 +0,0 @@ -# Byte-compiled / optimized / DLL files -__pycache__/ -*.py[codz] -*$py.class - -# C extensions -*.so - -# Distribution / packaging -.Python -build/ -develop-eggs/ -dist/ -downloads/ -eggs/ -.eggs/ -lib/ -lib64/ -parts/ -sdist/ -var/ -wheels/ -share/python-wheels/ -*.egg-info/ -.installed.cfg -*.egg -MANIFEST - -# PyInstaller -# Usually these files are written by a python script from a template -# before PyInstaller builds the exe, so as to inject date/other infos into it. -*.manifest -*.spec - -# Installer logs -pip-log.txt -pip-delete-this-directory.txt - -# Unit test / coverage reports -htmlcov/ -.tox/ -.nox/ -.coverage -.coverage.* -.cache -nosetests.xml -coverage.xml -*.cover -*.py.cover -.hypothesis/ -.pytest_cache/ -cover/ - -# Translations -*.mo -*.pot - -# Django stuff: -*.log -local_settings.py -db.sqlite3 -db.sqlite3-journal - -# Flask stuff: -instance/ -.webassets-cache - -# Scrapy stuff: -.scrapy - -# Sphinx documentation -docs/_build/ - -# PyBuilder -.pybuilder/ -target/ - -# Jupyter Notebook -.ipynb_checkpoints - -# IPython -profile_default/ -ipython_config.py - -# pyenv -# For a library or package, you might want to ignore these files since the code is -# intended to run in multiple environments; otherwise, check them in: -# .python-version - -# pipenv -# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. -# However, in case of collaboration, if having platform-specific dependencies or dependencies -# having no cross-platform support, pipenv may install dependencies that don't work, or not -# install all needed dependencies. -#Pipfile.lock - -# UV -# Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control. -# This is especially recommended for binary packages to ensure reproducibility, and is more -# commonly ignored for libraries. -#uv.lock - -# poetry -# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. -# This is especially recommended for binary packages to ensure reproducibility, and is more -# commonly ignored for libraries. -# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control -#poetry.lock -#poetry.toml - -# pdm -# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. -# pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python. -# https://pdm-project.org/en/latest/usage/project/#working-with-version-control -#pdm.lock -#pdm.toml -.pdm-python -.pdm-build/ - -# pixi -# Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control. -#pixi.lock -# Pixi creates a virtual environment in the .pixi directory, just like venv module creates one -# in the .venv directory. It is recommended not to include this directory in version control. -.pixi - -# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm -__pypackages__/ - -# Celery stuff -celerybeat-schedule -celerybeat.pid - -# SageMath parsed files -*.sage.py - -# Environments -.env -.envrc -.venv -env/ -venv/ -ENV/ -env.bak/ -venv.bak/ - -# Spyder project settings -.spyderproject -.spyproject - -# Rope project settings -.ropeproject - -# mkdocs documentation -/site - -# mypy -.mypy_cache/ -.dmypy.json -dmypy.json - -# Pyre type checker -.pyre/ - -# pytype static type analyzer -.pytype/ - -# Cython debug symbols -cython_debug/ - -# PyCharm -# JetBrains specific template is maintained in a separate JetBrains.gitignore that can -# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore -# and can be added to the global gitignore or merged into this file. For a more nuclear -# option (not recommended) you can uncomment the following to ignore the entire idea folder. -.idea/ - -# Abstra -# Abstra is an AI-powered process automation framework. -# Ignore directories containing user credentials, local state, and settings. -# Learn more at https://abstra.io/docs -.abstra/ - -# Visual Studio Code -# Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore -# that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore -# and can be added to the global gitignore or merged into this file. However, if you prefer, -# you could uncomment the following to ignore the entire vscode folder -.vscode/ - -# Ruff stuff: -.ruff_cache/ - -# PyPI configuration file -.pypirc - -# Cursor -# Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to -# exclude from AI features like autocomplete and code analysis. Recommended for sensitive data -# refer to https://docs.cursor.com/context/ignore-files -.cursorignore -.cursorindexingignore - -# Marimo -marimo/_static/ -marimo/_lsp/ -__marimo__/ diff --git a/dram_viz/rule_parser/.pre-commit-config.yaml b/dram_viz/rule_parser/.pre-commit-config.yaml deleted file mode 100644 index 4e0d9b6..0000000 --- a/dram_viz/rule_parser/.pre-commit-config.yaml +++ /dev/null @@ -1,31 +0,0 @@ -# This is the configuration for pre-commit, a local framework for managing pre-commit hooks -# Check out the docs at: https://pre-commit.com/ - -default_stages: [pre-commit] -repos: - - repo: https://github.com/rbubley/mirrors-prettier - rev: "v3.8.1" # Use the sha / tag you want to point at - hooks: - - id: prettier - additional_dependencies: - - prettier@2.1.2 - - "@prettier/plugin-xml@0.12.0" - - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v6.0.0 - hooks: - - id: check-case-conflict - - id: check-docstring-first - - id: check-executables-have-shebangs - - id: check-toml - - id: check-json - - id: detect-private-key - - id: end-of-file-fixer - - id: trailing-whitespace - - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.15.4 - hooks: - # Run the linter. - - id: ruff-check - args: [--fix] - # Run the formatter. - - id: ruff-format diff --git a/dram_viz/rule_parser/LICENSE b/dram_viz/rule_parser/LICENSE deleted file mode 100644 index f288702..0000000 --- a/dram_viz/rule_parser/LICENSE +++ /dev/null @@ -1,674 +0,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. 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But first, please read -. diff --git a/dram_viz/rule_parser/README.md b/dram_viz/rule_parser/README.md deleted file mode 100644 index 19654d1..0000000 --- a/dram_viz/rule_parser/README.md +++ /dev/null @@ -1,3 +0,0 @@ -# Rule-Parser - -DRAM LARK based Rule Parser for misciellaneous rules parsing tasks such as traits, summarize, and product. diff --git a/dram_viz/rule_parser/requirements.txt b/dram_viz/rule_parser/requirements.txt deleted file mode 100644 index d3bf3ad..0000000 --- a/dram_viz/rule_parser/requirements.txt +++ /dev/null @@ -1,4 +0,0 @@ -polars -lark -numpy -networkx diff --git a/dram_viz/rule_parser/requirements_dev.txt b/dram_viz/rule_parser/requirements_dev.txt deleted file mode 100644 index 57f4554..0000000 --- a/dram_viz/rule_parser/requirements_dev.txt +++ /dev/null @@ -1,7 +0,0 @@ -polars -lark -numpy -networkx -pytest -black -pre-commit diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 0000000..19aea56 --- /dev/null +++ b/pixi.lock @@ -0,0 +1,1296 @@ +version: 7 +platforms: +- name: linux-64 + virtual-packages: + - 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ukkonen ; extra == 'license' + requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 5554694..94a7fb7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,6 +20,7 @@ classifiers = [ "Operating System :: OS Independent", ] dynamic = ["version"] +requires-python = ">=3.12,<3.15" dependencies = [ 'bokeh >=3.0,<4.0', @@ -151,3 +152,16 @@ exclude_also = [ "logger = logging", ] + +[tool.pixi.workspace] +channels = ["conda-forge"] +platforms = ["linux-64"] + +[tool.pixi.pypi-dependencies] +dram_viz = { path = ".", editable = true } + +[tool.pixi.environments] +default = { solve-group = "default" } +dev = { features = ["dev"], solve-group = "default" } + +[tool.pixi.tasks] diff --git a/dram_viz/__init__.py b/src/__init__.py similarity index 79% rename from dram_viz/__init__.py rename to src/__init__.py index 5c0c0d1..c7e9f1b 100644 --- a/dram_viz/__init__.py +++ b/src/__init__.py @@ -1,5 +1,5 @@ try: - from dram_viz._version import __version__ + from src._version import __version__ except ImportError: # package not installed diff --git a/dram_viz/__main__.py b/src/__main__.py similarity index 50% rename from dram_viz/__main__.py rename to src/__main__.py index 7cfbdc4..792de85 100644 --- a/dram_viz/__main__.py +++ b/src/__main__.py @@ -1,4 +1,4 @@ -from dram_viz.make_product import main +from src.make_product import main if __name__ == "__main__": main() diff --git a/dram_viz/apps/__init__.py b/src/apps/__init__.py similarity index 100% rename from dram_viz/apps/__init__.py rename to src/apps/__init__.py diff --git a/dram_viz/apps/heatmap.py b/src/apps/heatmap.py similarity index 99% rename from dram_viz/apps/heatmap.py rename to src/apps/heatmap.py index 26f5185..37505e6 100644 --- a/dram_viz/apps/heatmap.py +++ b/src/apps/heatmap.py @@ -16,8 +16,8 @@ from bokeh.transform import factor_cmap, linear_cmap, log_cmap from panel_material_ui import Tree -from dram_viz.definitions import NO_TAXONOMY_RANKS, TAXONOMY_RANKS_REGEX -from dram_viz.rule_parser.src.rules import get_val_col +from src.definitions import NO_TAXONOMY_RANKS, TAXONOMY_RANKS_REGEX +from src.rule_parser.rules import get_val_col pn.extension("tabulator", "katex", template="bootstrap") diff --git a/dram_viz/data/.gitignore b/src/data/.gitignore similarity index 100% rename from dram_viz/data/.gitignore rename to src/data/.gitignore diff --git a/dram_viz/data/rules.tsv b/src/data/rules.tsv similarity index 100% rename from dram_viz/data/rules.tsv rename to src/data/rules.tsv diff --git a/dram_viz/data/rules_ag.tsv b/src/data/rules_ag.tsv similarity index 100% rename from dram_viz/data/rules_ag.tsv rename to src/data/rules_ag.tsv diff --git a/dram_viz/data/rules_aquatic.tsv b/src/data/rules_aquatic.tsv similarity index 100% rename from dram_viz/data/rules_aquatic.tsv rename to src/data/rules_aquatic.tsv diff --git a/dram_viz/data/rules_bgc.tsv b/src/data/rules_bgc.tsv similarity index 95% rename from dram_viz/data/rules_bgc.tsv rename to src/data/rules_bgc.tsv index c1134ee..b39cb3b 100644 --- a/dram_viz/data/rules_bgc.tsv +++ b/src/data/rules_bgc.tsv @@ -50,17 +50,17 @@ Fructose @Fructose Carbon Transformations Monosaccharide Hexose found in sucros Rhamnose @Rhamnose Carbon Transformations Monosaccharide Deoxyhexose commonly found in pectin (rhamnogalacturonans) and microbial polysaccharides. N-Acetylglucosamine (Glc-NAc) @N-Acetylglucosamine Carbon Transformations Monosaccharide Amino sugar found in chitin (fungal cell walls), bacterial peptidoglycan, and other glycoconjugates. SCFA-Propionate @Propionate-Final Carbon Transformations Low Molecular Weight Carbon -Scfa-Butyrate @Butyrate-Final Carbon Transformations Low Molecular Weight Carbon -Scfa-Acetate @Acetate-Final Carbon Transformations Low Molecular Weight Carbon +SCFA-Butyrate @Butyrate-Final Carbon Transformations Low Molecular Weight Carbon +SCFA-Acetate @Acetate-Final Carbon Transformations Low Molecular Weight Carbon Oxalate K01577 | K07749 Carbon Transformations Low Molecular Weight Carbon Formate K00656 Carbon Transformations Low Molecular Weight Carbon Methanol @Methanol Carbon Transformations Low Molecular Weight Carbon Ethanol/Alcohol @Ethanol Carbon Transformations Low Molecular Weight Carbon Photosynthesis @phototroph Energy Conservation Photosynthesis -Etc: Complex I Nadh Dehydrogenase at_least(9, PRESENCE, [K00330,K00331,K00332,K00333,K13378,K13380,K00334,K00335,K00336,K00337,K00338,K00339,K00340,K00341,K00342,K15863,K00343])|at_least(7, PRESENCE, [K05574,K05582,K05581,K05579,K05572,K05580,K05578,K05576,K05577,K05575,K05573,K05583,K05584,K05585])|at_least(4, PRESENCE, [K03878,K03879,K03880,K03881,K03882,K03883,K03884])|at_least(6, PRESENCE, [K03934,K03935,K03936,K03937,K03938,K03939,K03940,K03941,K03942,K03943,K03944])|at_least(7, PRESENCE, [K03945,K03946,K03947,K03948,K03949,K03950,K03951,K03952,K03953,K03954,K03955,K03956,K11352,K11353])|at_least(6, PRESENCE, [K03957,K03958,K03959,K03960,K03961,K03962,K03963,K03964,K03965,K03966,K11351])|at_least(3, PRESENCE, [K00346,K00347,K00348,K00349,K00350,K00351]) Energy Conservation Respiratory Electron Transport and ATP Synthesis -Etc: Complex II Succinate Dehydrogenase at_least(4, PRESENCE, [K00239,K00240,K00241,K00242,K00244,K00245,K00246,K00247,K18859,K18860])|at_least(2, PRESENCE, [K00234,K00235,K00236,K00237]) Energy Conservation Respiratory Electron Transport and ATP Synthesis Presence of a majority of an KEGG-derived Complex I variant, indicative of respiration -Etc: Complex III Cytochrome Bc1 Complex at_least(4, PRESENCE, [K00412,K00413,K00410,K00411,K03891,K03889,K03890])|at_least(4, PRESENCE, [K00414,K00415,K00416,K00417,K00418,K00419,K00420])|at_least(2, PRESENCE, [K03886,K03887,K03888]) Energy Conservation Respiratory Electron Transport and ATP Synthesis Presence of a majority of an KEGG-derived Complex II variant, indicative of respiration -Etc: Complex V Atpsynthase at_least(4, PRESENCE, [K02111,K02112,K02113,K02114,K02115,K02108,K02109,K02110])|at_least(5, PRESENCE, [K02117,K02118,K02119,K02120,K02121,K02122,K02107,K02123,K02124])|at_least(10, PRESENCE, [K02132,K02133,K02136,K02134,K02135,K02137,K02126,K02127,K02128,K02138,K02129,K01549,K02130,K02139,K02140,K02141,K02131,K02142,K02143,K02125])|at_least(7, PRESENCE, [K02145,K02147,K02148,K02149,K02150,K02151,K02152,K02144,K02154,K03661,K02155,K02146,K02153,K03662]) Energy Conservation Respiratory Electron Transport and ATP Synthesis Presence of a majority of an KEGG-derived Complex III variant, indicative of respiration +ETC: Complex I Nadh Dehydrogenase at_least(9, PRESENCE, [K00330,K00331,K00332,K00333,K13378,K13380,K00334,K00335,K00336,K00337,K00338,K00339,K00340,K00341,K00342,K15863,K00343])|at_least(7, PRESENCE, [K05574,K05582,K05581,K05579,K05572,K05580,K05578,K05576,K05577,K05575,K05573,K05583,K05584,K05585])|at_least(4, PRESENCE, [K03878,K03879,K03880,K03881,K03882,K03883,K03884])|at_least(6, PRESENCE, [K03934,K03935,K03936,K03937,K03938,K03939,K03940,K03941,K03942,K03943,K03944])|at_least(7, PRESENCE, [K03945,K03946,K03947,K03948,K03949,K03950,K03951,K03952,K03953,K03954,K03955,K03956,K11352,K11353])|at_least(6, PRESENCE, [K03957,K03958,K03959,K03960,K03961,K03962,K03963,K03964,K03965,K03966,K11351])|at_least(3, PRESENCE, [K00346,K00347,K00348,K00349,K00350,K00351]) Energy Conservation Respiratory Electron Transport and ATP Synthesis +ETC: Complex II Succinate Dehydrogenase at_least(4, PRESENCE, [K00239,K00240,K00241,K00242,K00244,K00245,K00246,K00247,K18859,K18860])|at_least(2, PRESENCE, [K00234,K00235,K00236,K00237]) Energy Conservation Respiratory Electron Transport and ATP Synthesis Presence of a majority of an KEGG-derived Complex I variant, indicative of respiration +ETC: Complex III Cytochrome Bc1 Complex at_least(4, PRESENCE, [K00412,K00413,K00410,K00411,K03891,K03889,K03890])|at_least(4, PRESENCE, [K00414,K00415,K00416,K00417,K00418,K00419,K00420])|at_least(2, PRESENCE, [K03886,K03887,K03888]) Energy Conservation Respiratory Electron Transport and ATP Synthesis Presence of a majority of an KEGG-derived Complex II variant, indicative of respiration +ETC: Complex V Atpsynthase at_least(4, PRESENCE, [K02111,K02112,K02113,K02114,K02115,K02108,K02109,K02110])|at_least(5, PRESENCE, [K02117,K02118,K02119,K02120,K02121,K02122,K02107,K02123,K02124])|at_least(10, PRESENCE, [K02132,K02133,K02136,K02134,K02135,K02137,K02126,K02127,K02128,K02138,K02129,K01549,K02130,K02139,K02140,K02141,K02131,K02142,K02143,K02125])|at_least(7, PRESENCE, [K02145,K02147,K02148,K02149,K02150,K02151,K02152,K02144,K02154,K03661,K02155,K02146,K02153,K03662]) Energy Conservation Respiratory Electron Transport and ATP Synthesis Presence of a majority of an KEGG-derived Complex III variant, indicative of respiration Oxygen - Low Affinity Use [percent(50,@CytochromeCOxidase)|percent(50,@CytochromeAa3600MenaquinolOxidase)|percent(50,@CytochromeOUbiquinolOxidase)] Respiratory Redox Processes Oxygen Reduction Oxygen - High Affinity Use [@percent50CytochromeBDUbiquinolOxidase|@percent50CytochromeCOxidaseCBB3] Respiratory Redox Processes Oxygen Reduction NO3 To NO2 @NarNitrateReductase|[@NapNitrateReductase] Respiratory Redox Processes Nitrogen Reduction @@ -71,8 +71,8 @@ DNRA, NO3 To NH4 @DNRA Respiratory Redox Processes Nitrogen Reduction DNRA NrfA only, NO2 To NH4 @nrfA Respiratory Redox Processes Nitrogen Reduction Aerobic Ammonium Oxidation @AerobicAmmoniaOxidizer Respiratory Redox Processes Nitrogen Oxidation Aerobic Nitrite Oxidation @NitriteOxidoreductase Respiratory Redox Processes Nitrogen Oxidation -Anaerobic Ammonia Oxidation Anammox @Annamox Respiratory Redox Processes Nitrogen Oxidation -Complete Ammonia Oxidation Comammox @Comammox Respiratory Redox Processes Nitrogen Oxidation +Anaerobic Ammonia Oxidation (Anammox) @Annamox Respiratory Redox Processes Nitrogen Oxidation +Complete Ammonia Oxidation (Comammox) @Comammox Respiratory Redox Processes Nitrogen Oxidation Iron Oxidation @IronOxidation Respiratory Redox Processes Iron Reduction and Oxidation Iron Reduction @IronReduction Respiratory Redox Processes Iron Reduction and Oxidation Sulfur Oxidation @sulfateoxidizer Respiratory Redox Processes Sulfur Reduction and Oxidation diff --git a/dram_viz/data/rules_eng_sys.tsv b/src/data/rules_eng_sys.tsv similarity index 100% rename from dram_viz/data/rules_eng_sys.tsv rename to src/data/rules_eng_sys.tsv diff --git a/dram_viz/data/rules_gut.tsv b/src/data/rules_gut.tsv similarity index 100% rename from dram_viz/data/rules_gut.tsv rename to src/data/rules_gut.tsv diff --git a/dram_viz/definitions.py b/src/definitions.py similarity index 100% rename from dram_viz/definitions.py rename to src/definitions.py diff --git a/dram_viz/make_product.py b/src/make_product.py similarity index 98% rename from dram_viz/make_product.py rename to src/make_product.py index 26f9487..107c52c 100644 --- a/dram_viz/make_product.py +++ b/src/make_product.py @@ -16,8 +16,8 @@ import polars as pl import polars.selectors as cs -from dram_viz.apps.heatmap import Dashboard -from dram_viz.definitions import ( +from src.apps.heatmap import Dashboard +from src.definitions import ( BACKUP_ALIAS_COLUMNS, BACKUP_FASTA_COLUMNS, BACKUP_GROUPBY_COLUMNS, @@ -27,13 +27,13 @@ DEFAULT_GROUPBY_COLUMN, DEFAULT_LABEL_COLUMN, ) -from dram_viz.processing.process_annotations import ( +from src.processing.process_annotations import ( build_tax_edge_df_pl, build_tax_tree_selected_recurse, build_taxonomy_df_pl, build_tree_pl, ) -from dram_viz.rule_parser.src.rules import ( +from src.rule_parser.rules import ( ID_EXPR_DICT, CompiledRules, build_present_map, @@ -245,7 +245,7 @@ def main( s = time.time() if common_rules_tsv is None: - common_rules_tsv = Path(__file__).parent / "rule_parser/src/rules_common.tsv" + common_rules_tsv = Path(__file__).parent / "rule_parser/rules_common.tsv" if rules_system and rules_tsv: raise click.BadArgumentUsage( diff --git a/dram_viz/processing/__init__.py b/src/processing/__init__.py similarity index 100% rename from dram_viz/processing/__init__.py rename to src/processing/__init__.py diff --git a/dram_viz/processing/process_annotations.py b/src/processing/process_annotations.py similarity index 98% rename from dram_viz/processing/process_annotations.py rename to src/processing/process_annotations.py index f96e570..221a2a0 100644 --- a/dram_viz/processing/process_annotations.py +++ b/src/processing/process_annotations.py @@ -5,7 +5,7 @@ import pandas as pd import polars as pl -from dram_viz.definitions import DEFAULT_FASTA_COLUMN +from src.definitions import DEFAULT_FASTA_COLUMN logger = logging.getLogger("dram.viz") diff --git a/dram_viz/rule_parser/src/__init__.py b/src/rule_parser/__init__.py similarity index 100% rename from dram_viz/rule_parser/src/__init__.py rename to src/rule_parser/__init__.py diff --git a/dram_viz/rule_parser/src/rules.lark b/src/rule_parser/rules.lark similarity index 100% rename from dram_viz/rule_parser/src/rules.lark rename to src/rule_parser/rules.lark diff --git a/dram_viz/rule_parser/src/rules.py b/src/rule_parser/rules.py similarity index 100% rename from dram_viz/rule_parser/src/rules.py rename to src/rule_parser/rules.py diff --git a/dram_viz/rule_parser/src/rules_common.tsv b/src/rule_parser/rules_common.tsv similarity index 96% rename from dram_viz/rule_parser/src/rules_common.tsv rename to src/rule_parser/rules_common.tsv index b6a3aa9..336f863 100644 --- a/dram_viz/rule_parser/src/rules_common.tsv +++ b/src/rule_parser/rules_common.tsv @@ -150,7 +150,7 @@ name alias rule HydrogenUse NiFe_group1 | NiFe_group2 | NiFe_group3 | NiFe_group4 | FeFe_groupA | FeFe_groupB | FeFe_groupC | FeFe_groupE | FeFe_groupF Fermenter not(@NegativeForFermenter) & [@Lactate-Final | @Ethanol | @Acetate-Final | @Butyrate-Final | @Propionate-Final] & [K00850 | K00873 | K01690 | K01625 | K00615 | K00616] - NegativeForFermenter @ETC50 | @Methanogen | @Denitrifier | @Sulfatereducer | @AerobicAmmoniaOxidizer | @Aerobe | @Microaerophillic | @phototroph + NegativeForFermenter @ETC50 | @Methanogen | @Denitrifier | @Sulfatereducer | @AerobicAmmoniaOxidizer | @Aerobe | @Microaerophillic | @phototroph | @Non-sulfate-sulfur-reduction | @IronReduction Denitrifier @ETC50 & [[@NarNitrateReductase | @NapNitrateReductase] | @NitriteReductase | @NitricOxideReductase | @NitrousOxideReductase] NitrousOxideReductase K00376 | EC:1.7.2.4 NitricOxideReductase K04561 | K15877 | EC:1.7.2.5 @@ -238,11 +238,11 @@ name alias rule Methanogen @MethylCoenzymeMReductase - MethylCoenzymeMReductase @McrAor3999 | K00400 | K00401 | K00402 | K03421 | K03422 + MethylCoenzymeMReductase @McrAor3999 | K00401 | K00402 notOtherMethanogen not(@OtherAjMethanogen) OtherAjMethanogen @Sulfatereducer | @Denitrifier | @AerobicAmmoniaOxidizer |@Comammox | @Annamox | @phototroph | @ETC60 - hydrogenotrophic [[[@McrAor3999] & @ReductiveAcetylCoAWoodLjungdahl_Archaeal_MethylOnly & @TetrahydromethanopterinSMethyltransferase_MTRcomplex & [ @Frh_hydrogenase |@Mvh_hydrogenase |@Eha_hydrogenase |@Ehb_hydrogenase |@Fdo_hydrogenase |@FormateDehydrogenase_1|@FdhF|@FdhAB ]] | [[tax(o__Methanoflorentales)|tax(g__Methanobacterium_A)|tax(g__Methanobacterium_C)|tax(g__Methanobacterium_E)|tax(g__Methanobacterium_F)|tax(g__Methanobacterium)|tax(g__Methanobrevibacter_A)|tax(g__Methanobrevibacter)|tax(g__Methanothermobacter_A)|tax(g__Methanothermobacter)|tax(g__Methanothermus)|tax(f__Methanobacteriaceae)|tax(g__Methanocella_A)|tax(g__Methanocella)|tax(g__Methanooceanicella)|tax(o__Methanococcales)|tax(o__Methanomicrobiales)|tax(g__Methanopyrus)|tax(o__Nezhaarchaeales)|tax(g__Methanolacinia)|tax(g__Methanobacterium_B)|tax(g__Methanobacterium_D)|tax(g__Methanosarcina)] & not(tax(g__Methanosphaera))]] & not([@McrAor3999] & [tax(g__Methanocomedens_A)|tax(g__Methanocomedens_B)|tax(g__Methanogaster_A)|tax(g__Methanogaster_B)|tax(g__Methanoperedens_A)|tax(g__Methanoperedens)|tax(g__ANME-1-THS)|tax(g__ANME1a)|tax(g__G60ANME1)|tax(g__Methanophaga)|tax(g__Methanovorans)|tax(g__Methanomarinus)|tax(g__Methanoxibalbensis)|tax(g__Methanospirare)|tax(g__Kmv04)|tax(g__Methanogaster_C)|tax(g__Methanogaster_D)|tax(g__CAZCRM01)|tax(g__UBA10536)|tax(g__Methanoxibalbensis)]) + hydrogenotrophic [[[@Methanogen] & @ReductiveAcetylCoAWoodLjungdahl_Archaeal_MethylOnly & @TetrahydromethanopterinSMethyltransferase_MTRcomplex & [ @Frh_hydrogenase |@Mvh_hydrogenase |@Eha_hydrogenase |@Ehb_hydrogenase |@Fdo_hydrogenase |@FormateDehydrogenase_1|@FdhF|@FdhAB ]] | [[tax(o__Methanoflorentales)|tax(g__Methanobacterium_A)|tax(g__Methanobacterium_C)|tax(g__Methanobacterium_E)|tax(g__Methanobacterium_F)|tax(g__Methanobacterium)|tax(g__Methanobrevibacter_A)|tax(g__Methanobrevibacter)|tax(g__Methanothermobacter_A)|tax(g__Methanothermobacter)|tax(g__Methanothermus)|tax(f__Methanobacteriaceae)|tax(g__Methanocella_A)|tax(g__Methanocella)|tax(g__Methanooceanicella)|tax(o__Methanococcales)|tax(o__Methanomicrobiales)|tax(g__Methanopyrus)|tax(o__Nezhaarchaeales)|tax(g__Methanolacinia)|tax(g__Methanobacterium_B)|tax(g__Methanobacterium_D)|tax(g__Methanosarcina)] & not(tax(g__Methanosphaera))]] & not([@Methanogen] & [tax(g__Methanocomedens_A)|tax(g__Methanocomedens_B)|tax(g__Methanogaster_A)|tax(g__Methanogaster_B)|tax(g__Methanoperedens_A)|tax(g__Methanoperedens)|tax(g__ANME-1-THS)|tax(g__ANME1a)|tax(g__G60ANME1)|tax(g__Methanophaga)|tax(g__Methanovorans)|tax(g__Methanomarinus)|tax(g__Methanoxibalbensis)|tax(g__Methanospirare)|tax(g__Kmv04)|tax(g__Methanogaster_C)|tax(g__Methanogaster_D)|tax(g__CAZCRM01)|tax(g__UBA10536)|tax(g__Methanoxibalbensis)]) ReductiveAcetylCoAWoodLjungdahl_Archaeal_MethylOnly at_least(4, PRESENCE, [ @FormylmethanofuranDehydrogenase, @Formylmethanofuran-Tetrahydromethanopterin-N-formyltransferase, @MethenyltetraydromethanopterinCyclohydrolase, @MethelenetetraydromethanopterinDehydrogenaseand510-MethenyltetrahydromethanopterinHydrogenase , @510-MethylenetetrahydromethanopterinReductase ]) TetrahydromethanopterinSMethyltransferase_MTRcomplex at_least(2,PRESENCE, [K00577,K00578,K00579,K00580,K00581,K00582,K00583,K00584]) Frh_hydrogenase at_least(2,PRESENCE, [K00440,K00441,K00442,K00443]) @@ -254,14 +254,25 @@ name alias rule FdhAB at_least(1,PRESENCE,[K00125,K22516]) McrAor3999 [McrA | K00399] - acetoclastic @McrAor3999 & at_least(1, PRESENCE, [K00193,K00194,K00197,K00198]) &[[K00925&K00625]|K01895] & [tax(g__Methanosarcina)|tax(f__Methanotrichaceae)] & not(@McrAor3999 & [tax(g__Methanocomedens_A)|tax(g__Methanocomedens_B)|tax(g__Methanogaster_A)|tax(g__Methanogaster_B)|tax(g__Methanoperedens_A)|tax(g__Methanoperedens)|tax(g__ANME-1-THS)|tax(g__ANME1a)|tax(g__G60ANME1)|tax(g__Methanophaga)|tax(g__Methanovorans)|tax(g__Methanomarinus)|tax(g__Methanoxibalbensis)|tax(g__Methanospirare)|tax(g__Kmv04)|tax(g__Methanogaster_C)|tax(g__Methanogaster_D)|tax(g__CAZCRM01)|tax(g__UBA10536)|tax(g__Methanoxibalbensis)]) + acetoclastic "@Methanogen + & at_least(1, PRESENCE, [K00193,K00194,K00197,K00198]) + & [ + [K00925&K00625] + | + K01895 + ] + & [tax(g__Methanosarcina)|tax(f__Methanotrichaceae)] + & not( + @Methanogen + & [tax(g__Methanocomedens_A)|tax(g__Methanocomedens_B)|tax(g__Methanogaster_A)|tax(g__Methanogaster_B)|tax(g__Methanoperedens_A)|tax(g__Methanoperedens)|tax(g__ANME-1-THS)|tax(g__ANME1a)|tax(g__G60ANME1)|tax(g__Methanophaga)|tax(g__Methanovorans)|tax(g__Methanomarinus)|tax(g__Methanoxibalbensis)|tax(g__Methanospirare)|tax(g__Kmv04)|tax(g__Methanogaster_C)|tax(g__Methanogaster_D)|tax(g__CAZCRM01)|tax(g__UBA10536)|tax(g__Methanoxibalbensis)] + )" ACS_CODH_complex at_least(1, PRESENCE, @ACS_CODH) ACS_CODH K00193,K00194,K00197,K00198 AcetateGenes @Ack_Pta | @AcetylCoASynthetase Ack_Pta K00925 & K00625 AcetylCoASynthetase K01895 - methylotroph [[@McrAor3999 & at_least(1, PRESENCE, [K04480,K14083,K16176,K16178,K25220,K16954,K25600,K25916,K26847])] | [tax(g__Methanobacterium_B)|tax(g__Methanobacterium_D)|tax(g__Methanosarcina)|tax(g__Methanodesulfokora)|tax(g__Methanosphaera)|tax(o__Methanomethylicales)|tax(c__Methanonatronarchaeia)|tax(g__Methanolobus)|tax(g__Methanomethylovorans)|tax(g__Methanohalobium)|tax(g__Methanohalophilus)|tax(g__Methanosalsum)|tax(g__Methermicoccus)|tax(g__Methanococcoides)|tax(g__Methanolapillus)|tax(g__MTP4)|tax(g__Methanimicrococcus)|tax(g__Methanofrustulum)|tax(o__Methanofastidiosales)|tax(o__Methanomassiliicoccales)|tax(f__Methanonatronarchaeaceae)]] & not(@McrAor3999 & [tax(g__Methanocomedens_A)|tax(g__Methanocomedens_B)|tax(g__Methanogaster_A)|tax(g__Methanogaster_B)|tax(g__Methanoperedens_A)|tax(g__Methanoperedens)|tax(g__ANME-1-THS)|tax(g__ANME1a)|tax(g__G60ANME1)|tax(g__Methanophaga)|tax(g__Methanovorans)|tax(g__Methanomarinus)|tax(g__Methanoxibalbensis)|tax(g__Methanospirare)|tax(g__Kmv04)|tax(g__Methanogaster_C)|tax(g__Methanogaster_D)|tax(g__CAZCRM01)|tax(g__UBA10536)|tax(g__Methanoxibalbensis)]) + methylotroph [[@Methanogen & at_least(1, PRESENCE, [K04480,K14083,K16176,K16178,K25220,K16954,K25600,K25916,K26847])] | [tax(g__Methanobacterium_B)|tax(g__Methanobacterium_D)|tax(g__Methanosarcina)|tax(g__Methanodesulfokora)|tax(g__Methanosphaera)|tax(o__Methanomethylicales)|tax(c__Methanonatronarchaeia)|tax(g__Methanolobus)|tax(g__Methanomethylovorans)|tax(g__Methanohalobium)|tax(g__Methanohalophilus)|tax(g__Methanosalsum)|tax(g__Methermicoccus)|tax(g__Methanococcoides)|tax(g__Methanolapillus)|tax(g__MTP4)|tax(g__Methanimicrococcus)|tax(g__Methanofrustulum)|tax(o__Methanofastidiosales)|tax(o__Methanomassiliicoccales)|tax(f__Methanonatronarchaeaceae)]] & not(@Methanogen & [tax(g__Methanocomedens_A)|tax(g__Methanocomedens_B)|tax(g__Methanogaster_A)|tax(g__Methanogaster_B)|tax(g__Methanoperedens_A)|tax(g__Methanoperedens)|tax(g__ANME-1-THS)|tax(g__ANME1a)|tax(g__G60ANME1)|tax(g__Methanophaga)|tax(g__Methanovorans)|tax(g__Methanomarinus)|tax(g__Methanoxibalbensis)|tax(g__Methanospirare)|tax(g__Kmv04)|tax(g__Methanogaster_C)|tax(g__Methanogaster_D)|tax(g__CAZCRM01)|tax(g__UBA10536)|tax(g__Methanoxibalbensis)]) mtxB K04480| K14083 |K16176 | K16178 |K25220 | K16954 AerobicMethanotroph @TRUEPmoA | @mmoX @@ -269,7 +280,7 @@ name alias rule TRUEPmoA pmoa_alpha_1 | pmoa_alpha_2 | pmoa_crenothrix | pmoa_gamma | pmoa_methyl_eth | pmoa_methylomirabilis | pmoa_verr | pmoa_actinobacteria_chloroflexota mmoX K16157 - anaerobic-methanotrophic-Archaea @McrAor3999 & [tax(g__Methanocomedens_A)|tax(g__Methanocomedens_B)|tax(g__Methanogaster_A)|tax(g__Methanogaster_B)|tax(g__Methanoperedens_A)|tax(g__Methanoperedens)|tax(g__ANME-1-THS)|tax(g__ANME1a)|tax(g__G60ANME1)|tax(g__Methanophaga)|tax(g__Methanovorans)|tax(g__Methanomarinus)|tax(g__Methanoxibalbensis)|tax(g__Methanospirare)|tax(g__Kmv04)|tax(g__Methanogaster_C)|tax(g__Methanogaster_D)|tax(g__CAZCRM01)|tax(g__UBA10536)|tax(g__Methanoxibalbensis)] + anaerobic-methanotrophic-Archaea @Methanogen & [tax(g__Methanocomedens_A)|tax(g__Methanocomedens_B)|tax(g__Methanogaster_A)|tax(g__Methanogaster_B)|tax(g__Methanoperedens_A)|tax(g__Methanoperedens)|tax(g__ANME-1-THS)|tax(g__ANME1a)|tax(g__G60ANME1)|tax(g__Methanophaga)|tax(g__Methanovorans)|tax(g__Methanomarinus)|tax(g__Methanoxibalbensis)|tax(g__Methanospirare)|tax(g__Kmv04)|tax(g__Methanogaster_C)|tax(g__Methanogaster_D)|tax(g__CAZCRM01)|tax(g__UBA10536)|tax(g__Methanoxibalbensis)] NOxorRed @ProbableNarNxr & not(@NitriteOxidoreductase) & not(@NarNitrateReductase) diff --git a/tests/test_heatmap_polars.py b/tests/test_heatmap_polars.py index eee5203..0fd5187 100644 --- a/tests/test_heatmap_polars.py +++ b/tests/test_heatmap_polars.py @@ -4,7 +4,7 @@ import polars as pl from bokeh.models import CategoricalColorMapper, LinearColorMapper, LogColorMapper -from dram_viz.apps.heatmap import heatmap +from src.apps.heatmap import heatmap class PolarsHeatmapTests(unittest.TestCase): diff --git a/tests/test_parsing.py b/tests/test_parsing.py index 922882e..cc9082a 100644 --- a/tests/test_parsing.py +++ b/tests/test_parsing.py @@ -2,7 +2,7 @@ import polars as pl -from dram_viz.rule_parser.src.rules import ( +from src.rule_parser.rules import ( And, Call, CompiledRules, diff --git a/tests/test_taxonomy_filter.py b/tests/test_taxonomy_filter.py index 05ce101..7a690d4 100644 --- a/tests/test_taxonomy_filter.py +++ b/tests/test_taxonomy_filter.py @@ -9,8 +9,8 @@ from panel.io.state import set_curdoc from panel_material_ui import Tree -from dram_viz.apps.heatmap import Dashboard -from dram_viz.processing.process_annotations import ( +from src.apps.heatmap import Dashboard +from src.processing.process_annotations import ( build_tax_edge_df_pl, build_tax_tree_selected_recurse, build_tree_pl,