diff --git a/.gitignore b/.gitignore index 12f98d2..7d486bc 100644 --- a/.gitignore +++ b/.gitignore @@ -34,3 +34,39 @@ Temporary Items # temporary files which can be created if a process still has a handle open of a deleted file .fuse_hidden* + +# KDE directory preferences +.directory + +# Linux trash folder which might appear on any partition or disk +.Trash-* + +# .nfs files are created when an open file is removed but is still being accessed +.nfs* + +# CLOJURE +.clerk + + +# AnW template +template/analysis/pbin + +# OCaml +template/analysis/_build/ + + +# Bazel +bazel-bin +bazel-out +bazel-template +bazel-testlogs + +MODULE.bazel.lock + +template/.cpcache + +template/analysis/renv + +_output + +*swp diff --git a/template/.LICENSE.template b/template/.LICENSE.template deleted file mode 100644 index aae54c9..0000000 --- a/template/.LICENSE.template +++ /dev/null @@ -1,23 +0,0 @@ -Copyright (c) 2021-2025 MAGMA pipeline authors, see https://doi.org/10.1371/journal.pcbi.1011648 - -This file is part of MAGMA pipeline, see https://github.com/TORCH-Consortium/MAGMA - -For quick overview of GPL-3 license, please refer -https://www.tldrlegal.com/license/gnu-general-public-license-v3-gpl-3 - -- You MUST keep this license with original authors in your copy -- You MUST acknowledge the original source of this software -- You MUST state significant changes made to the original software - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program . If not, see . diff --git a/template/.air.toml b/template/.air.toml deleted file mode 100644 index 52d0f59..0000000 --- a/template/.air.toml +++ /dev/null @@ -1,9 +0,0 @@ -# https://posit-dev.github.io/air/ -[format] -line-width = 80 -indent-width = 2 -indent-style = "space" -line-ending = "auto" -persistent-line-breaks = true -exclude = [] -default-exclude = true diff --git a/template/.bazelrc b/template/.bazelrc deleted file mode 100644 index e69de29..0000000 diff --git a/template/.bazelversion b/template/.bazelversion deleted file mode 100644 index 2b0aa21..0000000 --- a/template/.bazelversion +++ /dev/null @@ -1 +0,0 @@ -8.2.1 diff --git a/template/.dir-locals.el b/template/.dir-locals.el deleted file mode 100644 index 44f91fd..0000000 --- a/template/.dir-locals.el +++ /dev/null @@ -1,3 +0,0 @@ -(((nil . ((eval . (load-file (expand-file-name ".emacs.proj/project-setup.el" (projectile-project-root))))))) - (clojure-mode . ((cider-preferred-build-tool . clojure-cli) - (cider-clojure-cli-parameters . "-A:nextjournal/clerk")))) diff --git a/template/.dvc/config b/template/.dvc/config deleted file mode 100644 index 4cf322d..0000000 --- a/template/.dvc/config +++ /dev/null @@ -1,2 +0,0 @@ -[core] - autostage = true diff --git a/template/.dvcignore b/template/.dvcignore deleted file mode 100644 index e69de29..0000000 diff --git a/template/.editorconfig b/template/.editorconfig deleted file mode 100644 index c188c03..0000000 --- a/template/.editorconfig +++ /dev/null @@ -1,15 +0,0 @@ -root = true - -[*] -indent_style = space -indent_size = 4 -end_of_line = lf -charset = utf-8 -trim_trailing_whitespace = true -insert_final_newline = true - -[*.{yml,yaml,R,Rmd,r,rmd}] -indent_size = 2 - -[Makefile] -indent_style = tab diff --git a/template/.emacs.proj/project-setup.el b/template/.emacs.proj/project-setup.el deleted file mode 100644 index 69d103b..0000000 --- a/template/.emacs.proj/project-setup.el +++ /dev/null @@ -1,43 +0,0 @@ -;;; project-setup.el --- Description -*- lexical-binding: t; -*- -;; -;; Copyright (C) 2025 Abhinav Sharma -;; -;; Author: Abhinav Sharma -;; Maintainer: Abhinav Sharma -;; Created: May 25, 2025 -;; Modified: May 25, 2025 -;; Version: 0.0.1 -;; Keywords: abbrev bib c calendar comm convenience data docs emulations extensions faces files frames games hardware help hypermedia i18n internal languages lisp local maint mail matching mouse multimedia news outlines processes terminals tex text tools unix vc wp -;; Homepage: https://github.com/eklavya/project-setup -;; Package-Requires: ((emacs "24.3")) -;; -;; This file is not part of GNU Emacs. -;; -;;; Commentary: -;; -;; Description -;; -;;; Code: - - -(setq org-capture-templates - '(("e" "Experiment" entry (file "~/org/experiments.org") - "* Experiment: %^{Title} -:PROPERTIES: -:DATE: %U -:STATUS: planned -:END: -** Objective -%? -** Method -** Code -#+BEGIN_SRC python :results output -#+END_SRC -** Results -** Analysis -** Next Steps -"))) - - -(provide 'project-setup) -;;; project-setup.el ends here diff --git a/template/.envrc.template b/template/.envrc.template deleted file mode 100644 index 1c5ebb4..0000000 --- a/template/.envrc.template +++ /dev/null @@ -1,2 +0,0 @@ -export PATH="$PATH:$PWD/pbin" -export MISE_TASK_DIR=".mise/tasks" diff --git a/template/.fish/aliases.sh b/template/.fish/aliases.sh deleted file mode 100644 index b60af66..0000000 --- a/template/.fish/aliases.sh +++ /dev/null @@ -1,2 +0,0 @@ -alias gs 'git status' -alias gp 'git pull' diff --git a/template/.fish/completions.sh b/template/.fish/completions.sh deleted file mode 100644 index e69de29..0000000 diff --git a/template/.fish/config.fish b/template/.fish/config.fish deleted file mode 100644 index eba9040..0000000 --- a/template/.fish/config.fish +++ /dev/null @@ -1,27 +0,0 @@ -# fish/config.fish for project-specific Fish shell setup - -# Source global fish config if it exists (merge global and project configs) -if test -f ~/.config/fish/config.fish - source ~/.config/fish/config.fish -end - -# Set project-specific environment variable for starship -set -gx PROJECT_NAME "your_project" - -# Point Starship to the project-specific configuration -set -gx STARSHIP_CONFIG (dirname (status --current-filename))/starship.toml - -# Initialize Starship prompt for fish -starship init fish | source - -# Source project-specific aliases and functions -if test -f (dirname (status --current-filename))/aliases.fish - source (dirname (status --current-filename))/aliases.fish -end - -for f in (dirname (status --current-filename))/functions/*.fish - source $f -end - -# Use project-specific fish history -set -gx fish_history (dirname (status --current-filename))/history diff --git a/template/.fish/functions.sh b/template/.fish/functions.sh deleted file mode 100644 index e69de29..0000000 diff --git a/template/.fish/history b/template/.fish/history deleted file mode 100644 index e69de29..0000000 diff --git a/template/.fish/run_fish.sh b/template/.fish/run_fish.sh deleted file mode 100755 index a13b92e..0000000 --- a/template/.fish/run_fish.sh +++ /dev/null @@ -1,8 +0,0 @@ -#!/usr/bin/env bash -# Launch fish with project-specific config - -FISH_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/../.fish" && pwd)" -export XDG_CONFIG_HOME="$FISH_DIR" -export fish_history="$FISH_DIR/history" - -exec fish --init-command "source $FISH_DIR/config.fish" diff --git a/template/.fish/starship.toml b/template/.fish/starship.toml deleted file mode 100644 index 7a0cce3..0000000 --- a/template/.fish/starship.toml +++ /dev/null @@ -1,68 +0,0 @@ -# Starship prompt configuration for project-specific Fish shell setup - -# General prompt settings -add_newline = true - -[character] -success_symbol = "[➜](bold green) " -error_symbol = "[βœ—](bold red) " - -[git_branch] -symbol = "🌱 " -format = "[$symbol$branch]($style) " - -[git_status] -format = '([\[$all_status$ahead_behind\]]($style) )' -style = "yellow" - -[directory] -truncation_length = 3 -truncate_to_repo = true -read_only = " ο ½" -style = "bold blue" - -[python] -symbol = "🐍 " -pyenv_version_name = true -format = 'via [$symbol$version ($virtualenv)]($style) ' - -[julia] -symbol = "πŸ‘Ύ " -format = 'via [$symbol$version]($style) ' - -[nodejs] -symbol = "β¬’ " -format = 'via [$symbol$version]($style) ' - -[package] -symbol = "πŸ“¦ " -format = 'via [$symbol$version]($style) ' - -[env_var.PROJECT_NAME] -format = '[($env_value)]($style) ' -style = "bold yellow" -# You can set PROJECT_NAME env var in your fish config for display - -[conda] -symbol = "πŸ…’ " -format = '[$symbol$environment]($style) ' - -[docker_context] -symbol = "🐳 " -format = 'via [$symbol$context]($style) ' - -[cmd_duration] -format = "took [$duration]($style) " -style = "yellow" - -[time] -disabled = false -format = 'πŸ•™ [$time]($style) ' -time_format = "%T" -style = "bold cyan" - -[custom.vscode] -when = "test -n \"$VSCODE_PID\"" -command = "echo " -format = "[$output]($style) " -style = "bold purple" diff --git a/template/.hasrc b/template/.hasrc deleted file mode 100644 index 384f83a..0000000 --- a/template/.hasrc +++ /dev/null @@ -1,8 +0,0 @@ -# tools -git - -# interpreters -java -node -python -R diff --git a/template/.licenseheaders.json b/template/.licenseheaders.json deleted file mode 100644 index b7505a9..0000000 --- a/template/.licenseheaders.json +++ /dev/null @@ -1,24 +0,0 @@ -{ - "java": { - "extensions": [ - ".java", - ".scala", - ".groovy", - ".config", - ".nf", - ".jape", - ".js", - ".ts", - ".tsx" - ], - "keepFirst": "", - "blockCommentStartPattern": "^\\s*/\\*", - "blockCommentEndPattern": "\\*/\\s*$", - "lineCommentStartPattern": "^\\s*//", - "lineCommentEndPattern": "", - "headerStartLine": "/*\n", - "headerEndLine": " */\n", - "headerLinePrefix": " * ", - "headerLineSuffix": "" - } -} diff --git a/template/.markdownlint-cli2.yaml b/template/.markdownlint-cli2.yaml deleted file mode 100644 index cb6053b..0000000 --- a/template/.markdownlint-cli2.yaml +++ /dev/null @@ -1,4 +0,0 @@ -config: - line-length: false - no-duplicate-heading: - siblings_only: true diff --git a/template/.mise/tasks/build b/template/.mise/tasks/build deleted file mode 100644 index 54af8b6..0000000 --- a/template/.mise/tasks/build +++ /dev/null @@ -1,3 +0,0 @@ -#!/usr/bin/env bash -#MISE description="Build the CLI" -cargo build diff --git a/template/.mise/tasks/greet b/template/.mise/tasks/greet deleted file mode 100755 index f806285..0000000 --- a/template/.mise/tasks/greet +++ /dev/null @@ -1,16 +0,0 @@ -#!/usr/bin/env bash -set -e - -#MISE description="Greet a user with a message" -#USAGE flag "-g --greeting " help="The greeting word to use" { -#USAGE choices "hi" "hello" "hey" -#USAGE } -#USAGE flag "-u --user " help="The user to greet" -#USAGE flag "--dir " help="The directory to greet from" default="." -#USAGE complete "dir" run="find . -maxdepth 1 -type d" -#USAGE arg "" help="Greeting message" - -echo "all available options are in the env with the prefix 'usage_'" -env | grep usage_ - -echo "$usage_greeting, $usage_user! Your message is: $usage_message" diff --git a/template/.pre-commit-config.yaml b/template/.pre-commit-config.yaml deleted file mode 100644 index a2e7dfb..0000000 --- a/template/.pre-commit-config.yaml +++ /dev/null @@ -1,108 +0,0 @@ -# https://www.conventionalcommits.org/en/v1.0.0/ -repos: - - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v5.0.0 - hooks: - - id: trailing-whitespace - - id: end-of-file-fixer - - id: check-yaml - - id: check-merge-conflict - - repo: https://github.com/astral-sh/ruff-pre-commit - # Ruff version. - rev: v0.9.3 - hooks: - # Run the linter. - - id: ruff - types_or: [python, pyi, jupyter] - # Run the formatter. - - id: ruff-format - types_or: [python, pyi, jupyter] - - repo: https://github.com/felixgwilliams/nbwipers-pre-commit - rev: v0.6.1 - hooks: - - id: nbwipers-check-install - - id: nbwipers-large-files - - repo: https://github.com/crate-ci/typos - rev: v1.29.4 - hooks: - - id: typos - - repo: https://github.com/DavidAnson/markdownlint-cli2 - rev: v0.17.2 - hooks: - - id: markdownlint-cli2 - -#--------------- -# GENERATED BY DSO/DVC -#--------------- - -# fail_fast: false -# default_language_version: -# python: python3 -# default_stages: -# - pre-commit -# default_install_hook_types: -# - pre-commit -# - pre-push -# - post-checkout -# minimum_pre_commit_version: 2.16.0 -# exclude: '(dvc\.lock$|.*\.dvc$)' # these are auto-generated and potentially conflicting with autoformatting -# repos: -# - repo: https://github.com/pre-commit/pre-commit-hooks -# rev: v4.6.0 -# hooks: -# - id: detect-private-key -# - id: check-ast -# - id: end-of-file-fixer -# - id: mixed-line-ending -# args: [--fix=lf] -# - id: trailing-whitespace -# - id: check-case-conflict -# - id: check-merge-conflict -# args: [--assume-in-merge] - -# # for ipynb files in `src` directories: we never want to commit any output as rendered output files -# # are tracked by dvc -# - repo: https://github.com/kynan/nbstripout -# rev: "0.8.1" -# hooks: -# - id: nbstripout - -# - repo: local -# hooks: -# - id: lint -# name: Run dso lint -# entry: dso lint -# language: system -# stages: [pre-commit] -# - id: push -# name: Run dvc push -# entry: dvc git-hook pre-push -# require_serial: true -# language: system -# verbose: true -# always_run: true -# stages: [pre-push] - -# # These are hooks for automated formatting - we recommend them but don't enable them by default. - -# # Prettier formats Markdown, JSON, CSS, JS and others -# # - repo: https://github.com/rbubley/mirrors-prettier -# # rev: 'v3.4.2' -# # hooks: -# # - id: prettier - -# # Ruff formats Python files -# # - repo: https://github.com/astral-sh/ruff-pre-commit -# # rev: 'v0.9.4' -# # hooks: -# # - id: ruff -# # types_or: [python, pyi, jupyter] -# # args: [--fix, --exit-non-zero-on-fix] -# # - id: ruff-format -# # types_or: [python, pyi, jupyter] - -# # Styler formats R files -# # - repo: https://github.com/lorenzwalthert/precommit -# # rev: 'v0.4.3' -# # hooks: -# # - id: style-files diff --git a/template/.projectable.toml b/template/.projectable.toml deleted file mode 100644 index 2415b02..0000000 --- a/template/.projectable.toml +++ /dev/null @@ -1,13 +0,0 @@ -[filetree] -# Whether to show git diffs -use_git = true -# Ignore certain globs -ignore = [] -use_gitignore = true -refresh_time = 1000 -# Display directories before files -dirs_first = true -show_hidden_by_default = false -# Whether to show special commads in a fuzzy style. Alternative is a list-like -# view -special_commands_fuzzy = true diff --git a/template/.python-version.jinja b/template/.python-version.jinja deleted file mode 100644 index 60e9934..0000000 --- a/template/.python-version.jinja +++ /dev/null @@ -1 +0,0 @@ -{{python_version}} diff --git a/template/MODULE.bazel b/template/MODULE.bazel deleted file mode 100644 index 00bb183..0000000 --- a/template/MODULE.bazel +++ /dev/null @@ -1,6 +0,0 @@ -############################################################################### -# Bazel now uses Bzlmod by default to manage external dependencies. -# Please consider migrating your external dependencies from WORKSPACE to MODULE.bazel. -# -# For more details, please check https://github.com/bazelbuild/bazel/issues/18958 -############################################################################### diff --git a/template/README.md.jinja b/template/README.md.jinja index 6fc89de..1f4b418 100644 --- a/template/README.md.jinja +++ b/template/README.md.jinja @@ -11,5 +11,20 @@ just setup ``` +``` ++ f$ fossil init dotfiles.fossil (base) +project-id: a67acde347d45a93f66154f4ea8891c6e42071b3 +server-id: bfa086f6a809ec21933305a0acae99678f89d7cc +admin-user: abhi (initial password is "FYunALczah") + +... + +$ fossil add MODULE.bazel WORKSPACE bb.edn clay.edn deps.edn dev.cljs.edn dune-project dvc.yaml environment.yml jreleaser.yml mise* nbb.edn package.json pixi.toml.template pyproject.toml.jinja renv.lock .air.toml .bazel* .editorconfig .emacs.proj .envrc* .fish/* .hasrc .licenseheaders.json .LICENSE.template .markdownlint-cli2.yaml .mise .pre-commit-config.yaml .projectable.toml .python-version.jinja .Rprofile .vscode .dvc/config .dir-locals.el .dvcignore + +... + +$ rm ... +``` + Explore - https://deon.drivendata.org/ diff --git a/template/WORKSPACE b/template/WORKSPACE deleted file mode 100644 index e69de29..0000000 diff --git a/template/analysis/config/nextflow/params.yaml b/template/analysis/config/nextflow/params.yaml new file mode 100644 index 0000000..af42cbe --- /dev/null +++ b/template/analysis/config/nextflow/params.yaml @@ -0,0 +1,30 @@ +################################# !!! WARNING !!! ############################################# +# # +# params.yaml is AUTOMATICALLY GENERATED. DO NOT EDIT BY HAND or your changes might be lost. # +# # +# Instead, edit `params.in.yaml` and compile the changes using `dso compile-config`. # +# If you do not wish to use this feature, simply delete `params.in.yaml` # +# and remove this notice # +############################################################################################### + +dso: + quarto: # quarto configuration (will be placed in respective _quarto.yml by `dso exec quarto`) + before_script: '' # bash snippet to execute before running `dso exec quarto`, use this to setup environment modules etc. + author: + # please add a complete list of authors. If some authors only contributed to a certain workpackage/stage + # you can add the dso.quarto.author section in the respective params.in.yaml and they will be merged. + - name: Jane Doe + affiliations: + - Example Department + format: + html: + fig-format: svg + toc: true + code-fold: true + embed-resources: true + page-layout: full + execute: + warning: true + message: false + date: now + date-format: YYYY-MMM-DD diff --git a/template/analysis/data/data-{{short_name}}.org b/template/analysis/data/data-{{short_name}}.org index 44e58c5..cd1fd06 100644 --- a/template/analysis/data/data-{{short_name}}.org +++ b/template/analysis/data/data-{{short_name}}.org @@ -1,23 +1,23 @@ -* Dataset: +** DATASET: :PROPERTIES: :SOURCE: :UPDATED: :TAGS: dataset :END: -** Description +*** Description -** Schema +*** Schema | Column | Type | Description | |----------+--------+------------------| | user_id | int | User identifier | | name | string | User full name | -** Sample Data +*** Sample Data #+BEGIN_SRC python :results output import pandas as pd print(pd.read_csv("data.csv").head()) #+END_SRC -** Provenance +*** Provenance diff --git a/template/analysis/notebooks/experiments-{{short_name}}.org b/template/analysis/notebooks/experiments-{{short_name}}.org index 8991af0..f15f017 100644 --- a/template/analysis/notebooks/experiments-{{short_name}}.org +++ b/template/analysis/notebooks/experiments-{{short_name}}.org @@ -8,7 +8,7 @@ #+PROPERTY: CLOCK_INTO_DRAWER t #+PROPERTY: LOG_INTO_DRAWER t -* Experiments +** EXPERIMENTS :PROPERTIES: :EXPERIMENT_TYPE: all :STATUS: active @@ -16,7 +16,7 @@ :TAGS: experiments :END: -** Quick Reference +*** Quick Reference :PROPERTIES: :EXPERIMENT_TYPE: reference :STATUS: active @@ -24,27 +24,27 @@ :TAGS: reference :END: -*** Experiment Types +**** Experiment Types - [[#data-processing][Data Processing]] - [[#exploration][Exploration]] - [[#analysis][Analysis]] - [[#modeling][Modeling]] - [[#deployment][Deployment]] -*** Status Tags +**** Status Tags - TODO - IN_PROGRESS - DONE - FAILED - ARCHIVED -*** Priority Levels +**** Priority Levels - P0 (Critical) - P1 (High) - P2 (Medium) - P3 (Low) -** Templates +*** Templates :PROPERTIES: :EXPERIMENT_TYPE: template :STATUS: active @@ -52,7 +52,7 @@ :TAGS: templates :END: -*** Data Processing Template +**** Data Processing Template :PROPERTIES: :EXPERIMENT_TYPE: data :STATUS: template @@ -60,18 +60,18 @@ :TAGS: data_processing :END: -**** Objective +***** Objective - Process and prepare data for analysis - Ensure data quality and consistency - Create reproducible data pipeline -**** Input Data +***** Input Data - Source: - Format: - Size: - Last Updated: -**** Processing Steps +***** Processing Steps - [ ] Data loading - [ ] Source connection - [ ] Initial validation @@ -85,20 +85,20 @@ - [ ] Encoding - [ ] Feature scaling -**** Output +***** Output - Format: - Location: - Validation: -**** Dependencies +***** Dependencies - Libraries: - External Tools: - Compute Resources: -**** Notes +***** Notes - -*** Model Training Template +**** Model Training Template :PROPERTIES: :EXPERIMENT_TYPE: modeling :STATUS: template @@ -106,17 +106,17 @@ :TAGS: model_training :END: -**** Objective +***** Objective - Train and evaluate model performance - Optimize hyperparameters - Compare with baseline -**** Model Details +***** Model Details - Algorithm: - Version: - Framework: -**** Training Configuration +***** Training Configuration - [ ] Data split - [ ] Training: - [ ] Validation: @@ -131,7 +131,7 @@ - [ ] Distributed: - [ ] Checkpointing: -**** Evaluation Metrics +***** Evaluation Metrics - [ ] Primary metrics - [ ] Metric 1: - [ ] Metric 2: @@ -139,15 +139,15 @@ - [ ] Metric 1: - [ ] Metric 2: -**** Results +***** Results - Training time: - Best performance: - Comparison with baseline: -**** Notes +***** Notes - -*** Feature Engineering Template +**** Feature Engineering Template :PROPERTIES: :EXPERIMENT_TYPE: feature_engineering :STATUS: template @@ -155,17 +155,17 @@ :TAGS: feature_engineering :END: -**** Objective +***** Objective - Create new features - Select optimal feature set - Improve model performance -**** Input Features +***** Input Features - Original features: - Data types: - Missing values: -**** Feature Creation +***** Feature Creation - [ ] Domain features - [ ] Feature 1: - [ ] Feature 2: @@ -176,7 +176,7 @@ - [ ] Feature 1: - [ ] Feature 2: -**** Feature Selection +***** Feature Selection - [ ] Methods used - [ ] Correlation analysis - [ ] Importance ranking @@ -185,15 +185,15 @@ - [ ] Feature 1: - [ ] Feature 2: -**** Impact Analysis +***** Impact Analysis - [ ] Performance improvement: - [ ] Feature importance: - [ ] Computational cost: -**** Notes +***** Notes - -*** Model Deployment Template +**** Model Deployment Template :PROPERTIES: :EXPERIMENT_TYPE: deployment :STATUS: template @@ -201,12 +201,12 @@ :TAGS: deployment :END: -**** Objective +***** Objective - Deploy model to production - Ensure scalability and reliability - Monitor performance -**** Deployment Configuration +***** Deployment Configuration - [ ] Infrastructure - [ ] Cloud provider: - [ ] Instance type: @@ -216,7 +216,7 @@ - [ ] Containerization: - [ ] Load balancing: -**** Monitoring Setup +***** Monitoring Setup - [ ] Metrics - [ ] Performance metrics: - [ ] System metrics: @@ -226,7 +226,7 @@ - [ ] Error rates: - [ ] Resource usage: -**** Rollout Plan +***** Rollout Plan - [ ] Phases - [ ] Phase 1: - [ ] Phase 2: @@ -235,10 +235,10 @@ - [ ] Triggers: - [ ] Procedures: -**** Notes +***** Notes - -*** A/B Testing Template +**** A/B Testing Template :PROPERTIES: :EXPERIMENT_TYPE: analysis :STATUS: template @@ -246,12 +246,12 @@ :TAGS: ab_testing :END: -**** Objective +***** Objective - Compare model versions - Measure impact - Make data-driven decisions -**** Experiment Design +***** Experiment Design - [ ] Hypothesis - [ ] Null hypothesis: - [ ] Alternative hypothesis: @@ -262,7 +262,7 @@ - [ ] Start date: - [ ] End date: -**** Metrics +***** Metrics - [ ] Primary metrics - [ ] Metric 1: - [ ] Metric 2: @@ -270,7 +270,7 @@ - [ ] Metric 1: - [ ] Metric 2: -**** Analysis +***** Analysis - [ ] Statistical tests - [ ] Test type: - [ ] Significance level: @@ -279,15 +279,15 @@ - [ ] Effect size: - [ ] Confidence intervals: -**** Decision +***** Decision - [ ] Recommendation: - [ ] Next steps: - [ ] Documentation: -**** Notes +***** Notes - -** Data Processing +*** Data Processing :PROPERTIES: :EXPERIMENT_TYPE: data :STATUS: active @@ -295,7 +295,7 @@ :TAGS: data :END: -*** 00-raw +**** 00-raw :PROPERTIES: :EXPERIMENT_TYPE: data :STATUS: active @@ -303,21 +303,21 @@ :TAGS: raw_data :END: -**** Data Sources +***** Data Sources - [ ] Source 1 - [ ] Source 2 -**** Data Validation +***** Data Validation - [ ] Schema validation - [ ] Quality checks - [ ] Missing value analysis -**** Data Cleaning +***** Data Cleaning - [ ] Remove duplicates - [ ] Handle missing values - [ ] Outlier detection -*** 01-data +**** 01-data :PROPERTIES: :EXPERIMENT_TYPE: data :STATUS: active @@ -325,17 +325,17 @@ :TAGS: processed_data :END: -**** Data Transformation +***** Data Transformation - [ ] Normalization - [ ] Encoding - [ ] Feature scaling -**** Data Storage +***** Data Storage - [ ] Format selection - [ ] Storage location - [ ] Version control -** Exploration +*** Exploration :PROPERTIES: :EXPERIMENT_TYPE: exploration :STATUS: active @@ -343,7 +343,7 @@ :TAGS: exploration :END: -*** 02-exploration +**** 02-exploration :PROPERTIES: :EXPERIMENT_TYPE: exploration :STATUS: active @@ -351,17 +351,17 @@ :TAGS: eda :END: -**** Statistical Analysis +***** Statistical Analysis - [ ] Descriptive statistics - [ ] Distribution analysis - [ ] Correlation analysis -**** Visualization +***** Visualization - [ ] Univariate plots - [ ] Bivariate plots - [ ] Multivariate plots -** Analysis +*** Analysis :PROPERTIES: :EXPERIMENT_TYPE: analysis :STATUS: active @@ -369,7 +369,7 @@ :TAGS: analysis :END: -*** 03-analysis +**** 03-analysis :PROPERTIES: :EXPERIMENT_TYPE: analysis :STATUS: active @@ -377,17 +377,17 @@ :TAGS: statistical_analysis :END: -**** Hypothesis Testing +***** Hypothesis Testing - [ ] Test selection - [ ] Assumption checking - [ ] Results interpretation -**** Advanced Analysis +***** Advanced Analysis - [ ] Time series analysis - [ ] Spatial analysis - [ ] Network analysis -** Feature Engineering +*** Feature Engineering :PROPERTIES: :EXPERIMENT_TYPE: feature_engineering :STATUS: active @@ -395,7 +395,7 @@ :TAGS: features :END: -*** 04-feat_eng +**** 04-feat_eng :PROPERTIES: :EXPERIMENT_TYPE: feature_engineering :STATUS: active @@ -403,17 +403,17 @@ :TAGS: feature_engineering :END: -**** Feature Creation +***** Feature Creation - [ ] Domain features - [ ] Statistical features - [ ] Interaction features -**** Feature Selection +***** Feature Selection - [ ] Correlation analysis - [ ] Importance ranking - [ ] Dimensionality reduction -** Modeling +*** Modeling :PROPERTIES: :EXPERIMENT_TYPE: modeling :STATUS: active @@ -421,7 +421,7 @@ :TAGS: modeling :END: -*** 05-models +**** 05-models :PROPERTIES: :EXPERIMENT_TYPE: modeling :STATUS: active @@ -429,17 +429,17 @@ :TAGS: models :END: -**** Model Selection +***** Model Selection - [ ] Algorithm selection - [ ] Hyperparameter tuning - [ ] Cross-validation -**** Model Training +***** Model Training - [ ] Training setup - [ ] Performance metrics - [ ] Model comparison -** Interpretation +*** Interpretation :PROPERTIES: :EXPERIMENT_TYPE: interpretation :STATUS: active @@ -447,7 +447,7 @@ :TAGS: interpretation :END: -*** 06-interpretation +**** 06-interpretation :PROPERTIES: :EXPERIMENT_TYPE: interpretation :STATUS: active @@ -455,17 +455,17 @@ :TAGS: model_interpretation :END: -**** Model Insights +***** Model Insights - [ ] Feature importance - [ ] Partial dependence - [ ] SHAP values -**** Business Impact +***** Business Impact - [ ] ROI analysis - [ ] Risk assessment - [ ] Implementation strategy -** Deployment +*** Deployment :PROPERTIES: :EXPERIMENT_TYPE: deployment :STATUS: active @@ -473,7 +473,7 @@ :TAGS: deployment :END: -*** 07-deploy +**** 07-deploy :PROPERTIES: :EXPERIMENT_TYPE: deployment :STATUS: active @@ -481,17 +481,17 @@ :TAGS: deployment :END: -**** Model Serving +***** Model Serving - [ ] API design - [ ] Containerization - [ ] Scaling strategy -**** Monitoring +***** Monitoring - [ ] Performance monitoring - [ ] Drift detection - [ ] Alert system -** Reports +*** Reports :PROPERTIES: :EXPERIMENT_TYPE: reporting :STATUS: active @@ -499,7 +499,7 @@ :TAGS: reports :END: -*** 08-reports +**** 08-reports :PROPERTIES: :EXPERIMENT_TYPE: reporting :STATUS: active @@ -507,17 +507,17 @@ :TAGS: documentation :END: -**** Technical Documentation +***** Technical Documentation - [ ] Code documentation - [ ] API documentation - [ ] Architecture diagrams -**** User Documentation +***** User Documentation - [ ] User guides - [ ] Tutorials - [ ] FAQs -** References +*** References :PROPERTIES: :EXPERIMENT_TYPE: reference :STATUS: active @@ -525,12 +525,12 @@ :TAGS: references :END: -*** Documentation +**** Documentation - [[https://github.com/dfeich/org-babel-examples/blob/master/lisp/lisp-babel.org][Org Babel Examples]] - [[https://orgmode.org/manual/Working-with-Source-Code.html][Org Mode Source Code]] - [[https://orgmode.org/manual/Results-of-Evaluation.html][Org Mode Evaluation]] -*** Tools +**** Tools - [[https://jupyter.org/][Jupyter]] - [[https://quarto.org/][Quarto]] - [[https://www.r-project.org/][R]] @@ -552,21 +552,21 @@ :END: %U -**** Objective +***** Objective - -**** Methodology +***** Methodology - -**** Results +***** Results - -**** Conclusions +***** Conclusions - -**** Next Steps +***** Next Steps - [ ] -**** CLOCK: -**** LOG: "))) +***** CLOCK: +***** LOG: "))) #+END_SRC diff --git a/template/bb.edn b/template/bb.edn deleted file mode 100644 index 62683c3..0000000 --- a/template/bb.edn +++ /dev/null @@ -1,13 +0,0 @@ -{:tasks - {:requires ([babashka.fs :as fs]) - - test {:doc "Run tests" - :task (apply clojure "-M:test" *command-line-args*)} - - nrepl {:doc "Start REPL" - :task (if (fs/windows?) - (clojure "-M:nrepl") - (shell "rlwrap bb clojure -M:nrepl"))} - - uber {:doc "Build uberjar" - :task (clojure "-T:build uber")}}} diff --git a/template/clay.edn b/template/clay.edn deleted file mode 100644 index 53a51b3..0000000 --- a/template/clay.edn +++ /dev/null @@ -1,22 +0,0 @@ -;; Example: https://github.com/scicloj/clay/blob/3a4f3c29971f881725ec962a3b28c0ce603e6eb6/resources/clay-default.edn#L1 - -{:base-target-path "notebooks/compiled" - :subdirs-to-sync ["notebooks/src"] - :format [:html] - :show true - :browse true - :live-reload false - :run-quarto true - :quarto {:format {:html {:toc true - :toc-depth 4 - :theme :cosmo} - :revealjs {:theme :solarized - :navigation-mode :vertical - :transition :slide - :background-transition :fade - :incremental true}} - :code-block-background true} - :kindly/options {:datatables {:paging false - :scrollY 400 - :sPaginationType "full_numbers" - :order []}}} diff --git a/template/deps.edn b/template/deps.edn deleted file mode 100644 index 11bfe06..0000000 --- a/template/deps.edn +++ /dev/null @@ -1,46 +0,0 @@ -{:deps {;; CORE - org.clojure/clojure {:mvn/version "1.12.0"} - - io.github.pfeodrippe/wally {:mvn/version "0.0.4"} - - ;; parallel computing - ;;missionary/missionary {:mvn/version "b.44"} - - ;; SCICLOJ - scicloj/clojisr {:mvn/version "1.0.0"} - org.scicloj/kind-clerk {:mvn/version "1-alpha9"} - org.scicloj/kindly {:mvn/version "4-beta16"} - org.scicloj/noj {:mvn/version "2-beta16"} - org.scicloj/wolframite {:mvn/version "1.1.0"}} - - :aliases { - :fs-clojure {:classpath-overrides {org.clojure/clojure nil} - :extra-deps {com.github.flow-storm/clojure {:mvn/version "1.12.0-9"} - com.github.flow-storm/flow-storm-dbg {:mvn/version "4.4.3"}}} - - ;; Optional plugins you find yourself using regularly - :fs-web {:extra-deps {com.github.flow-storm/flow-storm-web-plugin {:mvn/version "1.0.0-beta"}} - :jvm-opts ["-Dclojure.storm.instrumentOnlyPrefixes.webPlugin=org.httpkit.server,ring.adapter.jetty,next.jdbc.result-set" - "-Dflowstorm.plugins.namespaces.webPlugin=flow-storm.plugins.web.all"]} - - :cljs {:extra-deps {org.clojure/clojurescript {:mvn/version "1.11.132"}}} - - :fig {:extra-deps {com.bhauman/figwheel-main {:mvn/version "0.2.20"} - com.bhauman/rebel-readline-cljs {:mvn/version "0.1.4"}} - :main-opts ["-m" "figwheel.main"]} - - :portal {:extra-deps {djblue/portal {:mvn/version "0.59.0"} - org.clojure/clojurescript {:mvn/version "1.10.844"}}} - - :debug {:extra-deps {djblue/flowstorm {:mvn/version "0.4.0"}}} - - :nextjournal/clerk {:extra-deps {org.babashka/cli {:mvn/version "0.7.52"} - org.scicloj/kind-clerk {:mvn/version "1-alpha9"} - io.github.nextjournal/clerk {:mvn/version "0.17.1102"}} - ;:exec-fn nextjournal.clerk/build! - #_#_:main-opts ["-m" "babashka.cli.exec"]}} - - :paths ["scripts/clojurescript/figwheel/src" - "scripts/clojurescript/src/figwheel/resources" - "scripts/clojurescript/src/figwheel/target"] - } diff --git a/template/dev.cljs.edn b/template/dev.cljs.edn deleted file mode 100644 index 72e98b6..0000000 --- a/template/dev.cljs.edn +++ /dev/null @@ -1 +0,0 @@ -{:main clojurescript.figwheel.src.hello-world.core} diff --git a/template/dotfiles.fossil b/template/dotfiles.fossil new file mode 100644 index 0000000..7abf368 Binary files /dev/null and b/template/dotfiles.fossil differ diff --git a/template/dune-project b/template/dune-project deleted file mode 100644 index 0a32580..0000000 --- a/template/dune-project +++ /dev/null @@ -1 +0,0 @@ -(lang dune 3.6) diff --git a/template/dvc.yaml b/template/dvc.yaml deleted file mode 100644 index dc11537..0000000 --- a/template/dvc.yaml +++ /dev/null @@ -1,50 +0,0 @@ -# # Feature/Training/Inference Pipelines - -# File Structure based on: - -# - -# ## Folder Structure - -# - src: source code -# - data: data extraction, data validation, data processing, data transformation, data save and export, etc. -# - model: model training, model evaluation, model validation, model save and export, etc. -# - inference: model prediction, model serving, model monitoring, etc. -# - pipelines: -# - feature_pipeline: takes as input raw data that it transforms into features (and labels) -# - training_pipeline: takes as input features and labels that it transforms into a model -# - inference_pipeline: takes new feature data and a trained model and makes predictions. - -# you could have multiple pipelines, for example: - -# - 3 feature pipelines that extract raw data from different sources and transform them into features and save it into a feature store. -# - 2 training pipelines that take the features from the feature store and train different models. -# - 3 inference pipeline that creates a model serving endpoint for each of the trained models and 1 batch -# inference pipeline that takes the features from the feature store and makes predictions in batch mode. - -# Finally is recommended to have a script that orchestrates the execution of the pipelines. This script should could be run in a cron job or a workflow orchestrator like Airflow, Prefect, Dagster, etc. - -stages: - data-extraction: - cmd: source src/cleanup.sh - deps: - - src/cleanup.sh - - data/raw - outs: - - data/clean.csv - # data-processing: - # data-transformation: - # data-save: - # data-export: - - # model-training: - # model-evaluation: - # model-validation: - # model-save: - # model-export: - # model-monitoring: - - # pipeline-feature-1: - # pipeline-feature-2: - # pipeline-training-1: - # pipeline-inference-1: diff --git a/template/environment.yml b/template/environment.yml deleted file mode 100644 index e69de29..0000000 diff --git a/template/jreleaser.yml b/template/jreleaser.yml deleted file mode 100644 index e39fa85..0000000 --- a/template/jreleaser.yml +++ /dev/null @@ -1,63 +0,0 @@ -environment: - properties: - artifactsDir: out/jreleaser/assemble/helloworld/archive - -matrix: - rows: - - { ext: '', platform: osx-aarch_64 } - - { ext: '', platform: osx-x86_64 } - - { ext: '', platform: linux-x86_64 } - #- { ext: '.exe', platform: windows-x86_64 } - -hooks: - script: - before: - - run: | - echo "Compiling {{ matrix.platform }}" - mkdir -p target/{{ matrix.platform }} - opam exec -- ocamlc -o target/{{ matrix.platform }}/helloworld{{ matrix.ext }} src/helloworld.ml - verbose: true - applyDefaultMatrix: true - verbose: true - filter: - includes: ['assemble'] - -project: - name: helloworld - description: HelloWorld in OCaml - longDescription: HelloWorld in OCaml - links: - homepage: https://github.com/jreleaser/helloworld-ocaml - authors: - - Andres Almiray - license: APACHE-2.0 - inceptionYear: 2023 - stereotype: CLI - -release: - github: - overwrite: true - changelog: - formatted: ALWAYS - preset: conventional-commits - contributors: - format: '- {{contributorName}}{{#contributorUsernameAsLink}} ({{.}}){{/contributorUsernameAsLink}}' - -assemble: - archive: - helloworld: - active: ALWAYS - formats: [ ZIP ] - applyDefaultMatrix: true - archiveName: '{{distributionName}}-{{projectVersion}}-{{ matrix.platform }}' - fileSets: - - input: 'target/{{ matrix.platform }}' - output: 'bin' - includes: [ 'helloworld{.exe,}' ] - - input: '.' - includes: [ 'LICENSE' ] - -distributions: - helloworld: - executable: - windowsExtension: exe diff --git a/template/misc/meetings-{{short_name}}.org b/template/misc/meetings-{{short_name}}.org index b93b08c..8c1556a 100644 --- a/template/misc/meetings-{{short_name}}.org +++ b/template/misc/meetings-{{short_name}}.org @@ -7,7 +7,7 @@ #+PROPERTY: PRIORITY all #+PROPERTY: TAGS all -* Meeting Notes +** MEETING NOTES :PROPERTIES: :MEETING_TYPE: template :PARTICIPANTS: all @@ -16,7 +16,7 @@ :TAGS: template :END: -** Quick Reference +*** Quick Reference :PROPERTIES: :MEETING_TYPE: reference :PARTICIPANTS: all @@ -25,27 +25,27 @@ :TAGS: reference :END: -*** Meeting Types +**** Meeting Types - [[#internal][Internal]] - [[#external][External]] - [[#project][Project]] - [[#review][Review]] - [[#planning][Planning]] -*** Status Tags +**** Status Tags - TODO - IN_PROGRESS - DONE - CANCELLED - DEFERRED -*** Priority Levels +**** Priority Levels - P0 (Critical) - P1 (High) - P2 (Medium) - P3 (Low) -** Meeting Templates +*** Meeting Templates :PROPERTIES: :MEETING_TYPE: template :PARTICIPANTS: all @@ -54,7 +54,7 @@ :TAGS: template :END: -*** Internal Meeting +**** Internal Meeting :PROPERTIES: :MEETING_TYPE: internal :PARTICIPANTS: team @@ -63,24 +63,24 @@ :TAGS: internal :END: -**** Agenda +***** Agenda - [ ] Item 1 - [ ] Item 2 - [ ] Item 3 -**** Notes +***** Notes - -**** Action Items +***** Action Items - [ ] -**** Decisions +***** Decisions - -**** Follow-up +***** Follow-up - [ ] -*** External Meeting +**** External Meeting :PROPERTIES: :MEETING_TYPE: external :PARTICIPANTS: external @@ -89,24 +89,24 @@ :TAGS: external :END: -**** Agenda +***** Agenda - [ ] Item 1 - [ ] Item 2 - [ ] Item 3 -**** Notes +***** Notes - -**** Action Items +***** Action Items - [ ] -**** Decisions +***** Decisions - -**** Follow-up +***** Follow-up - [ ] -*** Project Review +**** Project Review :PROPERTIES: :MEETING_TYPE: review :PARTICIPANTS: project @@ -115,24 +115,24 @@ :TAGS: review :END: -**** Agenda +***** Agenda - [ ] Progress Review - [ ] Blockers - [ ] Next Steps -**** Notes +***** Notes - -**** Action Items +***** Action Items - [ ] -**** Decisions +***** Decisions - -**** Follow-up +***** Follow-up - [ ] -** Recent Meetings +*** Recent Meetings :PROPERTIES: :MEETING_TYPE: all :PARTICIPANTS: all @@ -141,7 +141,7 @@ :TAGS: all :END: -*** TODAY +**** TODAY :PROPERTIES: :MEETING_TYPE: all :PARTICIPANTS: all @@ -150,7 +150,7 @@ :TAGS: all :END: -*** YESTERDAY +**** YESTERDAY :PROPERTIES: :MEETING_TYPE: all :PARTICIPANTS: all @@ -159,7 +159,7 @@ :TAGS: all :END: -** Meeting Archive +*** Meeting Archive :PROPERTIES: :MEETING_TYPE: all :PARTICIPANTS: all @@ -168,7 +168,7 @@ :TAGS: all :END: -*** 2024 +**** 2024 :PROPERTIES: :MEETING_TYPE: all :PARTICIPANTS: all @@ -177,7 +177,7 @@ :TAGS: all :END: -**** Q1 +***** Q1 :PROPERTIES: :MEETING_TYPE: all :PARTICIPANTS: all @@ -186,7 +186,7 @@ :TAGS: all :END: -***** January +****** January :PROPERTIES: :MEETING_TYPE: all :PARTICIPANTS: all @@ -195,7 +195,7 @@ :TAGS: all :END: -***** February +****** February :PROPERTIES: :MEETING_TYPE: all :PARTICIPANTS: all @@ -204,7 +204,7 @@ :TAGS: all :END: -***** March +****** March :PROPERTIES: :MEETING_TYPE: all :PARTICIPANTS: all @@ -213,7 +213,7 @@ :TAGS: all :END: -**** Q2 +***** Q2 :PROPERTIES: :MEETING_TYPE: all :PARTICIPANTS: all @@ -222,7 +222,7 @@ :TAGS: all :END: -***** April +****** April :PROPERTIES: :MEETING_TYPE: all :PARTICIPANTS: all @@ -231,7 +231,7 @@ :TAGS: all :END: -***** May +****** May :PROPERTIES: :MEETING_TYPE: all :PARTICIPANTS: all @@ -240,7 +240,7 @@ :TAGS: all :END: -***** June +****** June :PROPERTIES: :MEETING_TYPE: all :PARTICIPANTS: all @@ -264,18 +264,18 @@ :END: %U -**** Agenda +***** Agenda - [ ] -**** Notes +***** Notes - -**** Action Items +***** Action Items - [ ] -**** Decisions +***** Decisions - -**** Follow-up +***** Follow-up - [ ] "))) #+END_SRC diff --git a/template/mise.local.toml.template b/template/mise.local.toml.template deleted file mode 100644 index e69de29..0000000 diff --git a/template/mise.toml b/template/mise.toml deleted file mode 100644 index 0e86837..0000000 --- a/template/mise.toml +++ /dev/null @@ -1,8 +0,0 @@ -[env] -_.path = "./node_modules/.bin" -_.file = '.envrc' - - -[tasks.build] -description = "Build the CLI" -run = "cargo build" diff --git a/template/nbb.edn b/template/nbb.edn deleted file mode 100644 index 1c3f781..0000000 --- a/template/nbb.edn +++ /dev/null @@ -1 +0,0 @@ -{:deps { org.clojure/core.async {:mvn/version "1.8.741"} }} diff --git a/template/package-lock.json b/template/package-lock.json deleted file mode 100644 index 987f501..0000000 --- a/template/package-lock.json +++ /dev/null @@ -1,24 +0,0 @@ -{ - "name": "template", - "lockfileVersion": 3, - "requires": true, - "packages": { - "": { - "dependencies": { - "bibtex-tidy": "^1.14.0" - } - }, - "node_modules/bibtex-tidy": { - "version": "1.14.0", - "resolved": "https://registry.npmjs.org/bibtex-tidy/-/bibtex-tidy-1.14.0.tgz", - "integrity": "sha512-hTqn2R644Vgy503zRR9PvcFAKRPknvfauNCnQ4xtFgb8eeBHxWuP+gbgq/5/0fu6fOkVVxaELY3yFZmJOQ9HUg==", - "license": "MIT", - "bin": { - "bibtex-tidy": "bin/bibtex-tidy" - }, - "engines": { - "node": ">12" - } - } - } -} diff --git a/template/package.json b/template/package.json deleted file mode 100644 index 69a4bc3..0000000 --- a/template/package.json +++ /dev/null @@ -1,5 +0,0 @@ -{ - "dependencies": { - "bibtex-tidy": "^1.14.0" - } -} diff --git a/template/pixi.toml.template b/template/pixi.toml.template deleted file mode 100644 index c2cc246..0000000 --- a/template/pixi.toml.template +++ /dev/null @@ -1,22 +0,0 @@ -[workspace] -channels = ["conda-forge", "bioconda", "h2oai", "anaconda"] -name = "my-project" -platforms = ["linux-64", "osx-64"] - -[dependencies] -cowpy = "1.1.*" -python = "3.11.*" -ibis-duckdb = ">=10.5.0,<11" -great_tables = ">=0.14.0,<0.18" -h2o = "==3.46.0.7" -pandas = ">=2.2.3,<3" -seaborn = ">=0.13.2,<0.14" -matplotlib = ">=3.10.3,<4" -jupyterlab = ">=4.4.2,<5" -python-duckdb = "==1.3.0" -fastparquet = "==2024.11.0" -openjdk = "==21" -clojure="==1.12.0.1530" - -[tasks] -start = "python scripts/python/hello.py" diff --git a/template/project-{{short_name}}.org.jinja b/template/project-{{short_name}}.org.jinja index 78ab05e..d64ce78 100644 --- a/template/project-{{short_name}}.org.jinja +++ b/template/project-{{short_name}}.org.jinja @@ -9,3 +9,5 @@ #+transclude: [[file:writeup/writeup-{{short_name}}.org]] #+transclude: [[file:analysis/scripts/scripts-{{short_name}}.org]] + +#+transclude: [[file:misc/resources-{{short_name}}.org]] diff --git a/template/pyproject.toml.jinja b/template/pyproject.toml.jinja deleted file mode 100644 index d307fb5..0000000 --- a/template/pyproject.toml.jinja +++ /dev/null @@ -1,85 +0,0 @@ -[project] -name = "{{project_name}}" -version = "0.0.0" -description = "Add your description here" -readme = "README.md" -requires-python = ">={{python_version}}" -dependencies = [ - "dso-core>=0.9", - "ipykernel>=6.29.5", -] - -[tool.ruff] -line-length = 120 -target-version = "py{{ python_version|replace('.', '') }}" - -[tool.ruff.lint] -select = [ - "B", # flake8-bugbear - "BLE", # flake8-blind-except - "C4", # flake8-comprehensions - "D", # pydocstyle - "E", # Error detected by Pycodestyle - "F", # Errors detected by Pyflakes - "I", # isort - "RUF100", # Report unused noqa directives - "TID", # flake8-tidy-imports - "UP", # pyupgrade - "W", # Warning detected by Pycodestyle -] -ignore = [ - # Errors from function calls in argument defaults. These are fine when the result is immutable. - "B008", - # Missing docstring in public module - "D100", - # Missing docstring in public package - "D104", - # __magic__ methods are are often self-explanatory, allow missing docstrings - "D105", - # Missing docstring in __init__ - "D107", - ## Disable one in each pair of mutually incompatible rules - # We don’t want a blank line before a class docstring - "D203", - # We want docstrings to start immediately after the opening triple quote - "D213", - # first line should end with a period [Bug: doesn't work with single-line docstrings] - "D400", - # First line should be in imperative mood; try rephrasing - "D401", - # line too long -> we accept long comment lines; black gets rid of long code lines - "E501", - # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient - "E731", - # allow I, O, l as variable names -> I is the identity matrix - "E741", -] -unfixable = [ "F841" ] - - -[tool.ruff.lint.per-file-ignores] -"!{{module_name}}/**.py" = ["ANN", "D", "S101", "PLR2004", "T20"] - -[tool.ruff.lint.isort] -required-imports = ["from __future__ import annotations"] - -[tool.ruff.lint.pydocstyle] -convention = "google" - -[tool.typos] -files.extend-exclude = ["*.ipynb"] - -[tool.uv] -default-groups = ["dev", "lint"] - -[dependency-groups] -dev = [ - "nbwipers>=0.6.1", - "pytest>=8", - "pytest-cov>=6.0.0", - "pre-commit>=4.1.0", - "typos>=1.29.4", -] -lint = [ - "ruff>=0.9.3", -] diff --git a/template/renv.lock b/template/renv.lock deleted file mode 100644 index 49ea8f6..0000000 --- a/template/renv.lock +++ /dev/null @@ -1,23 +0,0 @@ -{ - "R": { - "Version": "4.3.1", - "Repositories": [ - { - "Name": "CRAN", - "URL": "https://packagemanager.posit.co/cran/latest" - } - ] - }, - "Packages": { - "renv": { - "Package": "renv", - "Version": "1.0.7", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "utils" - ], - "Hash": "397b7b2a265bc5a7a06852524dabae20" - } - } -}