amarantos 0.1.0__py3-none-any.whl

amarantos/core/loaders.py

@@ -0,0 +1,13 @@
+"""Load choice data from YAML files."""
+
+from amarantos.core.schemas import CHOICES_DIR, Choice
+
+
+def load_all_choices(domain: str | None = None) -> list[Choice]:
+    """Load all choices, optionally filtered by domain."""
+    if domain:
+        paths = sorted((CHOICES_DIR / domain).glob("*.yaml"))
+    else:
+        paths = sorted(CHOICES_DIR.glob("**/*.yaml"))
+
+    return [Choice.load(path) for path in paths]

amarantos/core/schemas.py

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+"""Schemas for choice data and user profiles."""
+
+import re
+from enum import StrEnum
+from pathlib import Path
+
+import attrs
+import dummio.yaml
+
+DATA_DIR = Path(__file__).parent.parent.parent / "data"
+CHOICES_DIR = DATA_DIR / "choices"
+
+# 95% CI uses 1.96 standard deviations
+Z_95 = 1.96
+
+
+def _name_to_filename(name: str) -> str:
+    """Convert a choice name to a valid filename."""
+    clean = name.lower()
+    clean = re.sub(r"\s*\([^)]*\)", "", clean)  # Remove parentheses content
+    clean = re.sub(r"[^a-z0-9]+", "_", clean)  # Replace non-alphanumeric with _
+    return clean.strip("_") + ".yaml"
+
+
+class Outcome(StrEnum):
+    """Health outcomes that can be measured -- at least in principle -- on a continuous scale."""
+
+    RELATIVE_MORTALITY_RISK = "Relative mortality risk"
+    DELAYED_AGING = "Years of delayed aging"
+    SUBJECTIVE_WELLBEING = "Subjective wellbeing - number of just-noticeable differences"
+
+
+@attrs.frozen
+class Effect:
+    """A Gaussian-distributed health effect estimate.
+
+    Attributes:
+        outcome: The health outcome being measured.
+        evidence: A summary of the evidence supporting this effect. Open-ended, but ideally includes things such as
+            the nature of the studies, sample sizes, and any relevant statistical measures, or first-principles
+            reasoning.
+        mean: The mean effect estimate.
+        std: The standard deviation of the effect estimate.
+    """
+
+    outcome: Outcome
+    mean: float
+    std: float
+    evidence: str = ""
+
+    @property
+    def ci_lower(self) -> float:
+        """Lower bound of 95% confidence interval."""
+        return self.mean - Z_95 * self.std
+
+    @property
+    def ci_upper(self) -> float:
+        """Upper bound of 95% confidence interval."""
+        return self.mean + Z_95 * self.std
+
+    @property
+    def is_beneficial(self) -> bool:
+        """Effect is beneficial if upper bound < 1.0."""
+        return self.ci_upper < 1.0
+
+    @property
+    def is_harmful(self) -> bool:
+        """Effect is harmful if lower bound > 1.0."""
+        return self.ci_lower > 1.0
+
+    @property
+    def is_uncertain(self) -> bool:
+        """Effect is uncertain if CI crosses 1.0."""
+        return self.ci_lower < 1.0 < self.ci_upper
+
+
+@attrs.frozen
+class Specification:
+    """Detailed specification of a wellness choice.
+
+    Attributes:
+        duration_h: Average duration of one session of the activity in hours.
+            For running, ~0.5. For taking a pill, ~0.001.
+        weekly_freq: How many times per week on average. Running might be 4,
+            taking a pill might be 7, fasting might be 1.
+        annual_cost_h: Total annual time cost including preparation, cleanup,
+            and actually doing the activity. Sleep optimization should count
+            bedtime ritual plus extra sleep time.
+        annual_cost_usd: Total annual dollar cost excluding time. For running,
+            maybe $100 for shoes.
+        description: Plain english description of the choice noting common
+            variations in implementation and citing evidence where available.
+    """
+
+    duration_h: float
+    weekly_freq: float
+    annual_cost_h: float
+    annual_cost_usd: float
+    description: str = ""
+
+
+@attrs.frozen
+class Choice:
+    """A wellness choice with effect estimates."""
+
+    domain: str
+    name: str
+    effects: tuple[Effect, ...]
+    specification: Specification
+    summary: str = ""
+
+    @property
+    def path(self) -> Path:
+        """Default path for this choice."""
+        return CHOICES_DIR / self.domain / _name_to_filename(self.name)
+
+    @classmethod
+    def load(cls, path: Path) -> "Choice":
+        """Load a choice from a YAML file."""
+        data = dummio.yaml.load(filepath=path)
+        data["effects"] = tuple(Effect(**e) for e in data["effects"])
+        data["specification"] = Specification(**data["specification"])
+        data.pop("literature", None)  # Remove legacy field if present
+        data.pop("annual_cost", None)  # Remove legacy field if present
+        return cls(**data)
+
+    def save(self, path: Path | None = None) -> None:
+        """Save this choice to a YAML file."""
+        if path is None:
+            path = self.path
+        data = {
+            "domain": self.domain,
+            "name": self.name,
+            "specification": attrs.asdict(self.specification),
+            "effects": [attrs.asdict(e) for e in self.effects],
+        }
+        if self.summary:
+            data["summary"] = self.summary
+        dummio.yaml.save(data, filepath=path)
+
+
+@attrs.frozen
+class User:
+    """User attributes for personalized recommendations."""
+
+    is_male: bool | None = None
+    age: int | None = None
+    height_cm: float | None = None
+    body_fat_pct: float | None = None
+    blood_pressure_systolic: int | None = None
+    is_vegan: bool | None = None
+    is_vegetarian: bool | None = None
+    diet_quality_pctl: float | None = None
+    exercise_cardio_pctl: float | None = None
+    exercise_resistance_pctl: float | None = None
+    sleep_hours: float | None = None

amarantos/rank.py

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+"""CLI to rank wellness choices by conservative lifespan impact estimate."""
+
+import click
+
+from amarantos.core.loaders import load_all_choices
+from amarantos.core.schemas import Choice, Effect, Outcome
+
+# 30th percentile z-score for normal distribution
+Z_30 = -0.524
+
+
+def get_effect_by_outcome(choice: Choice, outcome: Outcome) -> Effect | None:
+    """Extract a specific effect from a choice by outcome type."""
+    for effect in choice.effects:
+        if effect.outcome == outcome:
+            return effect
+    return None
+
+
+def percentile_30(effect: Effect) -> float:
+    """Calculate 30th percentile of effect estimate."""
+    return effect.mean + Z_30 * effect.std
+
+
+@click.command()
+@click.option(
+    "-n",
+    "--num-top-bottom",
+    type=int,
+    default=None,
+    help="Show only top N and bottom N choices",
+)
+@click.option(
+    "-d",
+    "--domain",
+    type=str,
+    default=None,
+    help="Filter by domain (e.g., 'diet', 'exercise')",
+)
+@click.option(
+    "--maxd",
+    type=int,
+    default=None,
+    help="Show only top N choices from each domain",
+)
+def main(num_top_bottom: int | None, domain: str | None, maxd: int | None) -> None:
+    """Rank wellness choices by 30th percentile lifespan impact."""
+    choices = load_all_choices(domain)
+
+    results: list[tuple[str, str, float, float, float]] = []
+    for choice in choices:
+        aging_effect = get_effect_by_outcome(choice, Outcome.DELAYED_AGING)
+        if aging_effect:
+            p30 = percentile_30(aging_effect)
+            results.append(
+                (
+                    choice.name,
+                    choice.domain,
+                    p30,
+                    choice.specification.annual_cost_usd,
+                    choice.specification.annual_cost_h,
+                )
+            )
+
+    # Sort by 30th percentile descending
+    results.sort(key=lambda x: x[2], reverse=True)
+
+    # Apply maxd filter if specified
+    if maxd is not None:
+        domain_counts: dict[str, int] = {}
+        filtered: list[tuple[str, str, float, float, float]] = []
+        for item in results:
+            d = item[1]
+            domain_counts[d] = domain_counts.get(d, 0) + 1
+            if domain_counts[d] <= maxd:
+                filtered.append(item)
+        results = filtered
+
+    # Header
+    click.echo()
+    click.echo(f"{'Choice':<40} {'P30 (years)':>12} {'$/year':>10} {'h/year':>10}")
+    click.echo("-" * 74)
+
+    if num_top_bottom is None:
+        for name, _, p30, cost_usd, cost_h in results:
+            click.echo(f"{name:<40} {p30:>+12.2f} {cost_usd:>10.0f} {cost_h:>10.0f}")
+    else:
+        click.echo(f"TOP {num_top_bottom}:")
+        for name, _, p30, cost_usd, cost_h in results[:num_top_bottom]:
+            click.echo(f"{name:<40} {p30:>+12.2f} {cost_usd:>10.0f} {cost_h:>10.0f}")
+
+        click.echo()
+        click.echo(f"BOTTOM {num_top_bottom}:")
+        for name, _, p30, cost_usd, cost_h in results[-num_top_bottom:]:
+            click.echo(f"{name:<40} {p30:>+12.2f} {cost_usd:>10.0f} {cost_h:>10.0f}")
+
+    click.echo()
+
+
+if __name__ == "__main__":
+    main()

amarantos-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: amarantos
+Version: 0.1.0
+Summary: Tips and tools for personal wellness and longevity
+Project-URL: Repository, https://github.com/zkurtz/amarantos
+Author-email: Zach Kurtz <zkurtz@gmail.com>
+License-Expression: MIT
+License-File: LICENSE
+Requires-Python: >=3.13
+Requires-Dist: attrs>=25.4
+Requires-Dist: click>=8.3.1
+Requires-Dist: dummio>=1.10.2
+Requires-Dist: matplotlib>=3.10.8
+Requires-Dist: numpy>=2.2.6
+Requires-Dist: pre-commit>=4.0.1
+Requires-Dist: ruamel-yaml>=0.19.1
+Description-Content-Type: text/markdown
+
+# Amarantos
+
+Tips and tools for personal wellness and longevity. *Amarantos* (ἀμάραντος) is Greek for "unfading" or "immortal" and is the root of *amaranth*—a flower known for retaining its color even dried.
+
+> **Warning: AI-Generated Content**
+>
+> This repository was generated with AI assistance and has not been thoroughly vetted by a human. References, claims, and code may contain errors or inaccuracies. Please double-check all information against primary sources and exercise critical judgment. Treat this as a starting point for careful research, not a definitive resource.
+
+## CLI Commands
+
+```bash
+# Rank all choices by 30th percentile lifespan impact
+amarantos
+
+# Filter by domain
+amarantos --domain exercise
+
+# Show only top/bottom 5
+amarantos -n 5
+
+# Show top 3 from each domain
+amarantos --maxd 3
+```
+
+## Awesome Longevity Resources
+
+A curated list of products, tools, and resources for personal wellness and longevity.
+
+### Knowledge & Research
+
+- [Examine.com](https://examine.com/) - Evidence-based supplement and nutrition information
+- [Peter Attia's The Drive](https://peterattiamd.com/) - Longevity-focused podcast and resources
+- [FoundMyFitness](https://www.foundmyfitness.com/) - Dr. Rhonda Patrick's research on nutrition and aging
+- [Fight Aging!](https://www.fightaging.org/) - Long-running blog covering aging research news
+- [LongevityWiki](https://longevitywiki.org/) - Community-curated longevity information
+- [Longevity Protocols](https://longevity-protocols.com/) - Personal project with AI-analyzed interventions (not peer-reviewed)
+- [Bryan Johnson's Blueprint](https://blueprint.bryanjohnson.com/) - Detailed self-experimentation protocol (note: sells supplements)
+
+### Scientific Databases & Journals
+
+- [DrugAge Database](https://genomics.senescence.info/drugs/) - Database of aging-related drugs
+- [Human Ageing Genomic Resources](https://genomics.senescence.info/) - Databases on aging-related genes
+- [GeroScience](https://www.springer.com/journal/11357) - Peer-reviewed aging research journal
+
+### Communities & DAOs
+
+- [r/longevity](https://www.reddit.com/r/longevity/) - Reddit community for longevity research
+- [VitaDAO](https://www.vitadao.com/) - Decentralized collective funding longevity research
+- [LessWrong Longevity Tag](https://www.lesswrong.com/tag/life-extension) - Rationalist perspectives on life extension
+
+### GitHub Repos & Awesome Lists
+
+- [awesome-longevity (atilatech)](https://github.com/atilatech/awesome-longevity) - Comprehensive longevity resources list
+- [awesome-longevity (Rejuve)](https://github.com/Rejuve/awesome-longevity) - Therapeutics, regenerative medicine, medical AI
+- [awesome-longevity-information](https://github.com/Laurentiu-Andronache/awesome-longevity-information) - Curated healthspan extension resources
+- [longevityTools](https://github.com/tgirke/longevityTools) - R package for longevity research analysis
+- [Longevity Genie](https://github.com/longevity-genie) - Open-source AI tools for longevity research
+
+### Tracking & Measurement
+
+- [Oura Ring](https://ouraring.com/) - Sleep and activity tracking
+- [Levels](https://www.levels.com/) - Continuous glucose monitoring
+- [InsideTracker](https://www.insidetracker.com/) - Blood biomarker analysis
+- [WHOOP](https://www.whoop.com/) - Strain and recovery monitoring
+
+### Academic & Research Institutions
+
+- [National Institute on Aging (NIA)](https://www.nia.nih.gov/) - NIH's primary aging research arm
+- [Buck Institute for Research on Aging](https://www.buckinstitute.org/) - Leading independent aging research institute
+- [Lifespan Research Institute (formerly SENS)](https://www.sens.org/) - Nonprofit focused on damage-repair approaches to aging
+- [Altos Labs](https://www.altoslabs.com/) - Well-funded cellular reprogramming research
+- [Calico Labs](https://www.calicolabs.com/) - Google/Alphabet's aging research company
+- [Stanford Center on Longevity](https://longevity.stanford.edu/) - Interdisciplinary longevity research
+- [American Federation for Aging Research (AFAR)](https://www.afar.org/) - Funds aging research and education
+
+## Software Tools
+
+### Installating amarantos
+
+TODO: get on pypi.
+
+```bash
+uv add amarantos
+```
+
+## Usage
+
+```python
+import amarantos
+
+amarantos.hello()
+```
+
+TODO: build something!

amarantos-0.1.0.dist-info/RECORD

@@ -0,0 +1,8 @@
+amarantos/rank.py,sha256=zRPcrmLM0DmWbpyny3cIDiLS1grnN3vDjAzQV5KbKMI,3080
+amarantos/core/loaders.py,sha256=cjP3ZonnEiih_AVRhduxj7M9JUA5aKYIkwEAC6zCD54,413
+amarantos/core/schemas.py,sha256=VB2635pK7v_ImH-CiTHOoDQt8HsgCX2j6iOpBjONLv0,5043
+amarantos-0.1.0.dist-info/METADATA,sha256=SmidSvIaAReZGrjslppQgIE4YXDMZ_pnuGXR3btzctY,4828
+amarantos-0.1.0.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+amarantos-0.1.0.dist-info/entry_points.txt,sha256=q8v2iCpAqD4w2NvptbQCsvdUQhq0yge1WyPaxNOdlwg,50
+amarantos-0.1.0.dist-info/licenses/LICENSE,sha256=yYmJX4hIj1EvCSZdWf20KULynADt84gULi3-Pqkb5l8,1067
+amarantos-0.1.0.dist-info/RECORD,,

amarantos-0.1.0.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: hatchling 1.28.0
+Root-Is-Purelib: true
+Tag: py3-none-any

amarantos-0.1.0.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+amarantos = amarantos.rank:main

amarantos-0.1.0.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Zach Kurtz
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.