# sci -- scientific computing aliases and functions

# ============================================================================
# QUICK COMPUTATION
# ============================================================================
alias q='qalc'
alias qc='qalc --terse'
alias oct='octave --quiet --eval'
alias bc='bc -l'

# ============================================================================
# CSV / DATA TOOLS
# ============================================================================
alias cl='csvlook'
alias cs='csvstat'
alias mlc='mlr --csv'
alias mlj='mlr --json'
alias mlp='mlr --icsv --opprint'
alias dm='datamash'
alias dmh='datamash -H'

# ============================================================================
# PAPER MANAGEMENT (papis)
# ============================================================================
alias pa='papis add --from arxiv'
alias pd='papis add --from doi'
alias po='papis open'
alias pe='papis edit'
alias pb='papis browse'

# ============================================================================
# arXiv
# ============================================================================
alias arxs='arxiv-search'

# ============================================================================
# SLURM (if on cluster)
# ============================================================================
alias sq='squeue -u $USER'
alias sqa='squeue -u $USER -o "%.8i %.9P %.30j %.2t %.10M %.6D %R"'

# ============================================================================
# FUNCTIONS
# ============================================================================

# calc -- python calculator with math imported
calc() {
    python3 -c "from math import *; print($*)"
}

# doi2bib -- DOI to BibTeX via content negotiation (zero dependencies)
doi2bib() {
    curl -sLH "Accept: application/x-bibtex" "https://doi.org/$1"
}

# doi2txt -- DOI to formatted citation
doi2txt() {
    curl -sLH "Accept: text/x-bibliography; style=apa" "https://doi.org/$1"
}

# arxdl -- download arXiv paper by ID
arxdl() {
    typeset id="$1"
    id="${id##*/abs/}"
    id="${id%.pdf}"
    python3 -c "
import arxiv
from urllib.request import urlretrieve
paper = next(arxiv.Client().results(arxiv.Search(id_list=['$id'])))
safe = ''.join(c if c.isalnum() or c in ' -_' else '' for c in paper.title)[:80]
fname = f'$id - {safe}.pdf'
urlretrieve(paper.pdf_url, fname)
print(f'Saved: {fname}')
"
}

# s2search -- Semantic Scholar search
s2search() {
    typeset query
    query=$(echo "$*" | tr ' ' '+')
    curl -s "https://api.semanticscholar.org/graph/v1/paper/search?query=$query&limit=10&fields=title,year,citationCount,url" | python3 -c "
import json, sys
data = json.load(sys.stdin)
for p in data.get('data', []):
    print(f\"{p.get('citationCount',0):>6}  {p.get('year','')}  {p['title']}\")
"
}

# s2related -- find related papers
s2related() {
    python3 -c "
from semanticscholar import SemanticScholar
s = SemanticScholar()
recs = s.get_recommended_papers('$1')
for r in recs[:10]:
    print(f'{r.citationCount:>6}  {r.year}  {r.title}')
"
}

# matmul -- matrix multiply
matmul() {
    python3 -c "import numpy as np; print(np.array($1) @ np.array($2))"
}

# eig -- eigenvalues
eig() {
    python3 -c "
import numpy as np
vals, vecs = np.linalg.eig(np.array($1))
print('Eigenvalues:', vals)
"
}

# det -- determinant
det() {
    python3 -c "import numpy as np; print(np.linalg.det(np.array($1)))"
}

# linsolve -- solve Ax=b
linsolve() {
    python3 -c "import numpy as np; print(np.linalg.solve(np.array($1), np.array($2)))"
}

# integrate -- numerical integration
integrate() {
    python3 -c "
from scipy.integrate import quad
import numpy as np
result, error = quad(lambda x: $1, $2, $3)
print(f'Result: {result:.10f}')
print(f'Error:  {error:.2e}')
"
}

# fft -- FFT from stdin data
fft() {
    python3 -c "
import numpy as np, sys
data = np.loadtxt(sys.stdin)
F = np.fft.rfft(data)
freq = np.fft.rfftfreq(len(data), d=1.0)
for f, a in zip(freq, np.abs(F)):
    print(f'{f:.6f}\t{a:.6f}')
"
}

# polyfit -- fit polynomial to two-column data from stdin
polyfit() {
    typeset degree="${1:-2}"
    python3 -c "
import numpy as np, sys
data = np.loadtxt(sys.stdin)
x, y = data[:,0], data[:,1]
coeffs = np.polyfit(x, y, $degree)
print('Coefficients:', coeffs)
p = np.poly1d(coeffs)
residuals = y - p(x)
print(f'R-squared: {1 - np.var(residuals)/np.var(y):.6f}')
"
}

# tplot -- terminal plot from stdin
tplot() {
    typeset title="${1:-Data}"
    python3 -c "
import plotext as plt, sys
data = [float(l.strip()) for l in sys.stdin if l.strip()]
plt.plot(data)
plt.title('$title')
plt.show()
"
}

# simbad -- look up astronomical object
simbad() {
    typeset ident
    ident=$(echo "$*" | tr ' ' '+')
    curl -s "https://simbad.u-strasbg.fr/simbad/sim-id?Ident=$ident&output.format=ASCII"
}

# apod -- NASA Astronomy Picture of the Day
apod() {
    typeset apod_date="${1:-$(date +%Y-%m-%d)}"
    curl -s "https://api.nasa.gov/planetary/apod?api_key=DEMO_KEY&date=$apod_date" | python3 -m json.tool
}

# fitsstats -- FITS file statistics
fitsstats() {
    python3 -c "
from astropy.io import fits
import numpy as np
data = fits.getdata('$1')
print(f'Shape: {data.shape}')
print(f'Min:   {np.nanmin(data):.4f}')
print(f'Max:   {np.nanmax(data):.4f}')
print(f'Mean:  {np.nanmean(data):.4f}')
print(f'Std:   {np.nanstd(data):.4f}')
"
}

# nf -- find notes with fzf
nf() {
    typeset notes_dir="${NOTES_DIR:-$HOME/notes}"
    typeset file
    file=$(find "$notes_dir" -name '*.md' -type f | \
        fzf --preview 'bat --color=always --style=numbers {}' \
            --preview-window=right:60%:wrap)
    [[ -n $file ]] && $EDITOR "$file"
}

# ns -- search note contents with fzf
ns() {
    typeset notes_dir="${NOTES_DIR:-$HOME/notes}"
    typeset match
    match=$(rg --line-number --no-heading --color=always "$1" "$notes_dir" | \
        fzf --ansi --delimiter=: \
            --preview 'bat --color=always --highlight-line {2} {1}')
    [[ -n $match ]] && $EDITOR "$(echo "$match" | cut -d: -f1)"
}

# nn -- new timestamped note
nn() {
    typeset notes_dir="${NOTES_DIR:-$HOME/notes}"
    typeset id=$(date +%Y%m%d%H%M%S)
    typeset title="${*:-Untitled}"
    typeset slug=$(echo "$title" | tr '[:upper:]' '[:lower:]' | tr ' ' '-' | tr -cd 'a-z0-9-')
    typeset file="$notes_dir/$id-$slug.md"
    printf -- '---\ntitle: %s\ndate: %s\ntags: []\n---\n\n' "$title" "$(date +%Y-%m-%dT%H:%M:%S)" > "$file"
    $EDITOR "$file"
}