feat(io): add CSV I/O (Fixes #228) - #237
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Signed-off-by: sonusharma6-dsa <ramprashadkumar11@gmail.com> (cherry picked from commit 7bbd6db) Signed-off-by: sonusharma6-dsa <ramprashadkumar11@gmail.com>
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…and fft modules Signed-off-by: sonusharma6-dsa <ramprashadkumar11@gmail.com>
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Pull request overview
Note
Copilot was unable to run its full agentic suite in this review.
This PR introduces a typed CSV reader/writer in mohu-io, implements core FFT utilities in mohu-fft, and includes a few small cleanups across supporting crates.
Changes:
- Added
mohu-io::csvmodule with typed inference, configurable read/write options, and convenience re-exports. - Implemented 1-D
fft/ifftplusfftfreq/fftshifthelpers inmohu-fft, with basic unit tests. - Minor formatting/metadata tweaks in
mohu-error,mohu-dtype, and workspace dependencies.
Reviewed changes
Copilot reviewed 13 out of 13 changed files in this pull request and generated 8 comments.
Show a summary per file
| File | Description |
|---|---|
| crates/mohu-io/src/csv.rs | Adds CSV reader/writer implementation and public API. |
| crates/mohu-io/src/lib.rs | Re-exports CSV API from crate root. |
| crates/mohu-io/tests/csv_tests.rs | Adds unit tests for CSV reader/writer behavior. |
| crates/mohu-io/Cargo.toml | Adds csv workspace dependency. |
| crates/mohu-fft/src/transform.rs | Implements fft/ifft wrappers around rustfft with normalization. |
| crates/mohu-fft/src/freq.rs | Implements fftfreq/rfftfreq/fftshift utilities with tests. |
| crates/mohu-fft/Cargo.toml | Adds cargo-machete ignored dependency metadata. |
| crates/mohu-error/src/test_utils.rs | Reorders imports and compacts panic formatting. |
| crates/mohu-error/src/reporter.rs | Formatting/alignment adjustments in formatting code paths. |
| crates/mohu-dtype/src/macros.rs | Removes an extra blank doc line. |
| crates/mohu-dtype/src/finfo.rs | Simplifies numeric casts in precision computations. |
| crates/mohu-dtype/src/dtype.rs | Adds FromStr impl for DType. |
| Cargo.toml | Adds workspace dependency on csv. |
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| /// Failure reported by the `csv` crate. | ||
| #[error("CSV parse error: {0}")] | ||
| Parse(#[from] csv::Error), |
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| let mut csv_reader = csv::ReaderBuilder::new() | ||
| .delimiter(self.opts.delimiter) | ||
| .has_headers(false) | ||
| .comment(self.opts.comment) | ||
| .trim(csv::Trim::All) | ||
| .flexible(true) | ||
| .from_reader(reader); |
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| let mut csv_writer = csv::WriterBuilder::new() | ||
| .delimiter(self.opts.delimiter) | ||
| .has_headers(false) | ||
| .terminator(csv::Terminator::Any(b'\n')) | ||
| .from_writer(&mut row_bytes); |
Comment on lines
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| impl std::str::FromStr for DType { | ||
| type Err = MohuError; | ||
|
|
||
| fn from_str(s: &str) -> Result<Self, Self::Err> { | ||
| DType::from_str(s) | ||
| } | ||
| } |
Comment on lines
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| pub use csv::{ | ||
| read_csv, write_csv, CsvError, CsvReader, CsvResult, CsvTable, CsvValue, CsvWriter, | ||
| ReadOptions, WriteOptions, | ||
| }; |
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| fn write_impl<W: Write>(&self, table: &CsvTable, mut writer: W) -> CsvResult<()> { | ||
| if self.opts.write_header && !table.headers.is_empty() { | ||
| self.write_row(&mut writer, table.headers.iter().map(String::as_str))?; | ||
| } | ||
|
|
||
| for row in &table.data { | ||
| let values = row.iter().map(|value| { | ||
| if matches!(value, CsvValue::Missing) { | ||
| self.opts.missing_repr.as_str().to_owned() | ||
| } else { | ||
| value.to_csv_string() | ||
| } | ||
| }).collect::<Vec<_>>(); | ||
|
|
||
| self.write_row(&mut writer, values.iter().map(String::as_str))?; | ||
| } | ||
|
|
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| Ok(()) | ||
| } | ||
|
|
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| fn write_row<W, I, S>(&self, writer: &mut W, fields: I) -> CsvResult<()> | ||
| where | ||
| W: Write, | ||
| I: IntoIterator<Item = S>, | ||
| S: AsRef<str>, | ||
| { | ||
| let mut row_bytes = Vec::new(); | ||
| { | ||
| let mut csv_writer = csv::WriterBuilder::new() | ||
| .delimiter(self.opts.delimiter) | ||
| .has_headers(false) | ||
| .terminator(csv::Terminator::Any(b'\n')) | ||
| .from_writer(&mut row_bytes); | ||
|
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| csv_writer.write_record(fields)?; | ||
| csv_writer.flush()?; | ||
| } |
| } | ||
|
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||
| /// Shift the zero-frequency component to the center of the spectrum. | ||
| pub fn fftshift<T: Clone>(mut v: Vec<T>) -> Vec<T> { |
| } | ||
|
|
||
| /// The inverse of `fftshift`. | ||
| pub fn ifftshift<T: Clone>(mut v: Vec<T>) -> Vec<T> { |
|
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📝 WalkthroughWalkthroughAdds a typed CSV reader/writer and tests (mohu-io), implements FFT frequency helpers and 1‑D FFT/IFFT (mohu-fft), introduces DType FromStr parsing, and applies broad formatting/reorganization and small API-adjacent edits across many crates plus Windows helper docs/script. ChangesCSV I/O Module
FFT Transform and Frequency Utilities
Type System and Error Handling Polish
Estimated code review effort 🎯 4 (Complex) | ⏱️ ~60 minutes Possibly related issues
✨ Finishing Touches🧪 Generate unit tests (beta)
|
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Actionable comments posted: 7
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Inline comments:
In `@crates/mohu-dtype/src/dtype.rs`:
- Around line 526-532: Remove the inherent parsing method DType::from_str (the
pub fn from_str on DType) and update all call sites to use the FromStr trait
implementation instead; specifically change any direct calls to
DType::from_str(s) in the TryFrom<&str> impls and the serde Deserialize code to
either s.parse::<DType>() or <DType as std::str::FromStr>::from_str(s) so the
trait implementation is used and error types (MohuError) are preserved.
In `@crates/mohu-fft/src/freq.rs`:
- Around line 23-24: Update the docstring for rfftfreq to accurately describe
its behavior: state that unlike fftfreq, rfftfreq returns only the non-negative
frequency bins (length n/2 + 1 for even n, floor(n/2) + 1 generally) for
real-input transforms, and clarify that it does not return the
negative-frequency counterparts; reference the function name rfftfreq and
fftfreq so readers know which behavior differs.
- Line 66: Replace the exact equality check on the float vector with
tolerance-based comparison: change the assertion that uses assert_eq!(f,
vec![0.0, 0.25, -0.5, -0.25]) to use moh_testing::approx::assert_allclose! so
the Vec<f64> in variable f is compared with the expected vec using approximate
(tolerance) comparison; keep the same expected values and use the macro path
moh_testing::approx::assert_allclose! to avoid adding new imports.
In `@crates/mohu-io/src/csv.rs`:
- Around line 156-162: The column() method and write_impl() in CsvTable assume
every row has length ncols and directly index row[idx], which can panic or
produce ragged output for non-rectangular tables; update column(), write_impl(),
and any public constructors/mutators that can create CsvTable.data so they
validate row widths or guard accesses: in column() iterate rows and use get(idx)
(or skip/return None for rows too short) and return Option<Vec<&CsvValue>> only
when all rows contain that index; in write_impl() validate each row length
against ncols (either pad, skip, or error) before emitting and return a Result
to propagate width errors; ensure CsvTable invariants are restored/checked on
construction and mutation so data and ncols remain consistent.
- Around line 13-47: Replace the local CsvError/CsvResult types and all manual
Err returns in this module with the project-wide MohuError from mohu-error:
remove the CsvError enum and CsvResult alias, change function return types to
Result<..., MohuError>, and convert places that currently propagate errors or
use `return Err(...)` to use `?` with `.context("...")` or `.with_context(||
"...")` to add operation-specific context; replace validation-style `return
Err(...)` with `ensure!(condition, "message with {}", arg)` and use
`bail!("message with {}", arg)` for early error returns so code uses
MohuError-compatible macros (bail!/ensure!) and context wrapping throughout
(including the other referenced blocks).
In `@crates/mohu-io/src/lib.rs`:
- Around line 6-9: Add a root-level doc comment above the pub use re-export
block that documents the CSV public API (read_csv, write_csv, CsvError,
CsvReader, CsvResult, CsvTable, CsvValue, CsvWriter, ReadOptions, WriteOptions)
and include at least one `# Example` code block demonstrating basic usage (e.g.,
reading or writing a CSV using read_csv/write_csv). Ensure the doc comment is
placed immediately above the existing `pub use csv::{ ... }` line and describes
the purpose of the re-exports and a minimal, compile-ready example showing how a
consumer would call one of the re-exported functions or types.
In `@crates/mohu-io/tests/csv_tests.rs`:
- Around line 39-40: The test uses exact equality on a float value
(assert_eq!(table.data[0][2], CsvValue::Float(9.5))) which violates the
float-comparison guideline; replace this with a call to
moh_testing::approx::assert_allclose by extracting the f64 from table.data[0][2]
(matching on CsvValue::Float) and passing the actual f64 and the expected 9.5 to
assert_allclose (optionally with a small tolerance), ensuring you import
moh_testing::approx::assert_allclose or fully qualify the call.
🪄 Autofix (Beta)
Fix all unresolved CodeRabbit comments on this PR:
- Push a commit to this branch (recommended)
- Create a new PR with the fixes
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📒 Files selected for processing (13)
Cargo.tomlcrates/mohu-dtype/src/dtype.rscrates/mohu-dtype/src/finfo.rscrates/mohu-dtype/src/macros.rscrates/mohu-error/src/reporter.rscrates/mohu-error/src/test_utils.rscrates/mohu-fft/Cargo.tomlcrates/mohu-fft/src/freq.rscrates/mohu-fft/src/transform.rscrates/mohu-io/Cargo.tomlcrates/mohu-io/src/csv.rscrates/mohu-io/src/lib.rscrates/mohu-io/tests/csv_tests.rs
💤 Files with no reviewable changes (1)
- crates/mohu-dtype/src/macros.rs
Comment on lines
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| impl std::str::FromStr for DType { | ||
| type Err = MohuError; | ||
|
|
||
| fn from_str(s: &str) -> Result<Self, Self::Err> { | ||
| DType::from_str(s) | ||
| } | ||
| } |
There was a problem hiding this comment.
CI-blocking clippy error: inherent from_str method conflicts with FromStr trait.
The pipeline shows a clippy::should_implement_trait error at line 463 because both an inherent method DType::from_str and this FromStr trait implementation exist. CI runs with -D warnings, so this blocks the build.
The FromStr trait is the idiomatic Rust approach for parsing from strings. Remove the inherent from_str method at line 463 and update all call sites (lines 536-544 TryFrom impls, line 559 serde deserialize) to use the trait via .parse() or qualify as <DType as FromStr>::from_str(s).
🔧 Proposed fix
Step 1: Delete the inherent method at lines 463-510 (the entire pub fn from_str block).
Step 2: Update call sites to use the trait. For example, the TryFrom<&str> impl at line 538 becomes:
impl TryFrom<&str> for DType {
type Error = MohuError;
- fn try_from(s: &str) -> MohuResult<Self> { DType::from_str(s) }
+ fn try_from(s: &str) -> MohuResult<Self> { s.parse() }
}Similarly, update line 543 and line 559 (serde).
As per coding guidelines: "MSRV: 1.85 in clippy.toml — CI runs -D warnings for zero warnings allowed. Fix clippy, do not #[allow] unless the lint is genuinely wrong, and document why."
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@crates/mohu-dtype/src/dtype.rs` around lines 526 - 532, Remove the inherent
parsing method DType::from_str (the pub fn from_str on DType) and update all
call sites to use the FromStr trait implementation instead; specifically change
any direct calls to DType::from_str(s) in the TryFrom<&str> impls and the serde
Deserialize code to either s.parse::<DType>() or <DType as
std::str::FromStr>::from_str(s) so the trait implementation is used and error
types (MohuError) are preserved.
Comment on lines
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+47
| use thiserror::Error; | ||
|
|
||
| /// Errors produced while reading or writing CSV data. | ||
| #[derive(Debug, Error)] | ||
| pub enum CsvError { | ||
| /// Underlying I/O failure. | ||
| #[error("I/O error: {0}")] | ||
| Io(#[from] std::io::Error), | ||
|
|
||
| /// Failure reported by the `csv` crate. | ||
| #[error("CSV parse error: {0}")] | ||
| Parse(#[from] csv::Error), | ||
|
|
||
| /// UTF-8 conversion failed while producing a `String` output. | ||
| #[error("UTF-8 conversion error: {0}")] | ||
| Utf8(#[from] std::string::FromUtf8Error), | ||
|
|
||
| /// No header or data rows were found. | ||
| #[error("empty file: no records found")] | ||
| EmptyFile, | ||
|
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| /// A data row had a different number of columns than expected. | ||
| #[error("row {row} has {got} columns, expected {expected}")] | ||
| ColumnMismatch { | ||
| /// 1-based row index within the data section. | ||
| row: usize, | ||
| /// Expected number of columns. | ||
| expected: usize, | ||
| /// Actual number of columns. | ||
| got: usize, | ||
| }, | ||
| } | ||
|
|
||
| /// Result type used by CSV reader and writer operations. | ||
| pub type CsvResult<T> = Result<T, CsvError>; |
There was a problem hiding this comment.
Align this module with the repository error-handling contract.
This code introduces CsvError/CsvResult, uses manual return Err(...), and propagates fallible ops without required context. That breaks the project-wide error model and will make cross-crate error reporting inconsistent.
As per coding guidelines, "Use MohuError from mohu-error everywhere for error handling", "Wrap error context with .context(\"what was being attempted\") or .with_context(|| ...)", and "Use bail! and ensure! macros from mohu-error — not manual return Err(...)."
Also applies to: 194-201, 223-226, 263-267, 338-347
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@crates/mohu-io/src/csv.rs` around lines 13 - 47, Replace the local
CsvError/CsvResult types and all manual Err returns in this module with the
project-wide MohuError from mohu-error: remove the CsvError enum and CsvResult
alias, change function return types to Result<..., MohuError>, and convert
places that currently propagate errors or use `return Err(...)` to use `?` with
`.context("...")` or `.with_context(|| "...")` to add operation-specific
context; replace validation-style `return Err(...)` with `ensure!(condition,
"message with {}", arg)` and use `bail!("message with {}", arg)` for early error
returns so code uses MohuError-compatible macros (bail!/ensure!) and context
wrapping throughout (including the other referenced blocks).
Comment on lines
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+162
| pub fn column(&self, idx: usize) -> Option<Vec<&CsvValue>> { | ||
| if idx >= self.ncols { | ||
| return None; | ||
| } | ||
|
|
||
| Some(self.data.iter().map(|row| &row[idx]).collect()) | ||
| } |
There was a problem hiding this comment.
Guard against non-rectangular CsvTable to prevent panics and ragged writes.
column() directly indexes rows (row[idx]) and write_impl() emits rows without width validation. Because CsvTable fields are public, inconsistent row widths can panic or silently produce malformed CSV.
Suggested hardening patch
pub fn column(&self, idx: usize) -> Option<Vec<&CsvValue>> {
if idx >= self.ncols {
return None;
}
-
- Some(self.data.iter().map(|row| &row[idx]).collect())
+ self.data.iter().map(|row| row.get(idx)).collect()
}- for row in &table.data {
+ for (row_index, row) in table.data.iter().enumerate() {
+ if row.len() != table.ncols {
+ return Err(CsvError::ColumnMismatch {
+ row: row_index + 1,
+ expected: table.ncols,
+ got: row.len(),
+ });
+ }
let values = row.iter().map(|value| {
if matches!(value, CsvValue::Missing) {
self.opts.missing_repr.as_str().to_owned()
} else {
value.to_csv_string()
}
}).collect::<Vec<_>>();Also applies to: 355-365
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@crates/mohu-io/src/csv.rs` around lines 156 - 162, The column() method and
write_impl() in CsvTable assume every row has length ncols and directly index
row[idx], which can panic or produce ragged output for non-rectangular tables;
update column(), write_impl(), and any public constructors/mutators that can
create CsvTable.data so they validate row widths or guard accesses: in column()
iterate rows and use get(idx) (or skip/return None for rows too short) and
return Option<Vec<&CsvValue>> only when all rows contain that index; in
write_impl() validate each row length against ncols (either pad, skip, or error)
before emitting and return a Result to propagate width errors; ensure CsvTable
invariants are restored/checked on construction and mutation so data and ncols
remain consistent.
Comment on lines
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to
+9
| pub use csv::{ | ||
| read_csv, write_csv, CsvError, CsvReader, CsvResult, CsvTable, CsvValue, CsvWriter, | ||
| ReadOptions, WriteOptions, | ||
| }; |
There was a problem hiding this comment.
🛠️ Refactor suggestion | 🟠 Major | ⚡ Quick win
Add root-level docs for the new CSV re-exports.
These newly exposed public API items in src/lib.rs should include a doc comment with at least one # Example block.
As per coding guidelines, "Public API items need doc comments with at least one # Example block."
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@crates/mohu-io/src/lib.rs` around lines 6 - 9, Add a root-level doc comment
above the pub use re-export block that documents the CSV public API (read_csv,
write_csv, CsvError, CsvReader, CsvResult, CsvTable, CsvValue, CsvWriter,
ReadOptions, WriteOptions) and include at least one `# Example` code block
demonstrating basic usage (e.g., reading or writing a CSV using
read_csv/write_csv). Ensure the doc comment is placed immediately above the
existing `pub use csv::{ ... }` line and describes the purpose of the re-exports
and a minimal, compile-ready example showing how a consumer would call one of
the re-exported functions or types.
Comment on lines
+39
to
+40
| assert_eq!(table.data[0][2], CsvValue::Float(9.5)); | ||
| } |
There was a problem hiding this comment.
Use approximate float comparison in this test.
This assertion currently relies on exact f64 equality through assert_eq!; switch it to mohu_testing::approx::assert_allclose.
As per coding guidelines, "Float comparisons in tests must use mohu_testing::approx::assert_allclose — never assert_eq! on f32 or f64."
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@crates/mohu-io/tests/csv_tests.rs` around lines 39 - 40, The test uses exact
equality on a float value (assert_eq!(table.data[0][2], CsvValue::Float(9.5)))
which violates the float-comparison guideline; replace this with a call to
moh_testing::approx::assert_allclose by extracting the f64 from table.data[0][2]
(matching on CsvValue::Float) and passing the actual f64 and the expected 9.5 to
assert_allclose (optionally with a small tolerance), ensuring you import
moh_testing::approx::assert_allclose or fully qualify the call.
Signed-off-by: GitHub Copilot <noreply@github.com>
Signed-off-by: GitHub Copilot <noreply@github.com>
Signed-off-by: GitHub Copilot <noreply@github.com>
There was a problem hiding this comment.
Actionable comments posted: 1
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Inline comments:
In @.github/workflows/ci.yml:
- Line 1: The CI YAML was flattened into one line and contains a UTF-8 BOM and
garbled characters which breaks parsing; open the workflow text (look for the
top-level workflow name and jobs like dco, fmt, clippy, build) and restore it to
a proper multi-line YAML document by removing the BOM and any stray garbled
bytes/characters, reinserting newlines and indentation so keys (name:, on:,
env:, jobs:, etc.) and job blocks (dco -> steps -> - uses:) are valid YAML, and
ensure the DCO step uses christophebedard/dco-check@0.5.1 exactly; validate by
running a YAML linter or `act`/GitHub Actions YAML parser to confirm no "mapping
values" errors remain.
🪄 Autofix (Beta)
Fix all unresolved CodeRabbit comments on this PR:
- Push a commit to this branch (recommended)
- Create a new PR with the fixes
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Run ID: ea246b79-c519-4115-9b02-ddab37ac3160
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Signed-off-by: sonusharma6-dsa <ramprashadkumar11@gmail.com>
Signed-off-by: sonusharma6-dsa <ramprashadkumar11@gmail.com>
Signed-off-by: sonusharma6-dsa <ramprashadkumar11@gmail.com>
Signed-off-by: sonusharma6-dsa <ramprashadkumar11@gmail.com>
Signed-off-by: sonusharma6-dsa <ramprashadkumar11@gmail.com>
Signed-off-by: sonusharma6-dsa <ramprashadkumar11@gmail.com>
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Adds CSV read/write support to mohu-io with configurable delimiters, header handling, missing value inference, and memory-efficient parsing.\n\nFiles added/changed: crates/mohu-io/src/csv.rs, crates/mohu-io/src/lib.rs, crates/mohu-io/Cargo.toml, Cargo.toml, crates/mohu-io/tests/csv_tests.rs.\n\nNote: I attempted to run cargo test -p mohu-io locally but encountered Windows linker/toolchain issues (MSVC link.exe not found and GNU dlltool bfd mismatch). Please run CI to validate tests.\n\nFixes #228
Summary by CodeRabbit
New Features
Tests
Documentation