Merge subcrates into a single library crate.

This commit unfortunately doesn't appear to speed up the time it takes
to compile before testing. Using `--lib` with `cargo test`, however,
does allow *most* tests to be compiled faster; a few integration tests
won't be run though.

Don't use re-exported dependencies. This means there will be a bit more
bookkeeping down the line to ensure that e.g. the same version of Marlu
is used across dependencies, but I prefer to have all dependencies made
explicit as well as available normally in the code.

Use "lto = "thin"". This makes performance slightly better and decreases
the size of the binary.

Make many types private (i.e. not public). In theory this allows for
more optimisation opportunities, but more importantly more easily
reveals what code isn't being used.

Restructure CLI arguments and tests. Calibration arguments are now much
more similar to other CLI args. True cargo integration tests require the
hyperdrive binary.

Fix some clippy lints (e.g. the `parse_from` trait method used on a
clap-enabled struct was often passed a &[], when [] was enough).

Fix some error variants not being used (either use them as intended or
delete them).

Replace `cexp` with `Complex::cis` and remove other unused math
functions. Depend on num-complex 0.4.1 because that's the version that
introduced `Complex::cis`.

.github/workflows/coverage.yml

@@ -1,16 +1,13 @@
 ---
 name: Generate Coverage report
 
-# Based on https://github.com/actions-rs/meta/blob/master/recipes/quickstart.md
-
-# Do this on every push, but don't double up on tags
 on:
   push:
     tags-ignore:
       - '**'
     pull_request:
     branches:
-    - '**'
+      - '**'
 
 env:
   CARGO_TERM_COLOR: always
@@ -21,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout sources
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
@@ -53,22 +50,20 @@ jobs:
           override: true
           components: llvm-tools-preview
 
-      - name: install cargo-llvm-cov
-        run: cargo install cargo-llvm-cov
+      # https://lib.rs/crates/cargo-llvm-cov#readme-continuous-integration
+      - name: Install cargo-llvm-cov
+        uses: taiki-e/install-action@cargo-llvm-cov
 
       - name: Get the beam HDF5 file
         run: curl http://ws.mwatelescope.org/static/mwa_full_embedded_element_pattern.h5 -o mwa_full_embedded_element_pattern.h5
 
       - name: Generate test lcov coverage into coverage/ dir
         run: |
           export MWA_BEAM_FILE=$(realpath mwa_full_embedded_element_pattern.h5)
-
-          mkdir -p coverage
-          cargo llvm-cov --all-targets --workspace --exclude mwa_hyperdrive_cuda --no-default-features --locked --lcov --output-path coverage/coverage.lcov
-          # this uses the result of the previous run to generate a text summary
-          cargo llvm-cov --no-run
+          cargo llvm-cov --workspace --lcov --output-path lcov.info
 
       - name: Upload reports to codecov.io
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v3
         with:
-          token: ${{ secrets.CODECOV_TOKEN }}
+          files: lcov.info
+          fail_ci_if_error: true

.github/workflows/releases.yml

@@ -53,7 +53,6 @@ jobs:
           curl https://raw.githubusercontent.com/HDFGroup/hdf5/develop/COPYING -o COPYING-hdf5
           curl https://raw.githubusercontent.com/liberfa/erfa/master/LICENSE -o LICENSE-erfa
           curl https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/License.txt -o LICENSE-cfitsio
-          cp cuda/LICENSE-NVIDIA .
           cp .github/workflows/releases-readme.md README.md
 
           cargo build --release --locked --no-default-features --features=hdf5-static,erfa-static,cfitsio-static

.github/workflows/run-tests.yml

@@ -69,20 +69,10 @@ jobs:
 
       # Can't test with CUDA, no GPUs available in CI
       - name: Run tests
-        run: |
-          cargo test
-          cd common  && cargo test --locked && cd ..
-          cd beam    && cargo test --locked && cd ..
-          # cd cuda    && cargo test --locked && cd ..
-          cd srclist && cargo test --locked && cd ..
+        run: cargo test --locked
 
       - name: Run ignored tests
-        run: |
-          cargo test -- --ignored
-          cd common  && cargo test --locked -- --ignored && cd ..
-          cd beam    && cargo test --locked -- --ignored && cd ..
-          # cd cuda    && cargo test --locked -- --ignored && cd ..
-          cd srclist && cargo test --locked -- --ignored && cd ..
+        run: cargo test --locked -- --ignored
 
       - name: Minimum-specified Rust version works
         run: |

CHANGELOG.md

@@ -0,0 +1,14 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic
+Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.2.1] - Unreleased
+### Changed
+- Use "lto = "thin"". This makes performance slightly better and decreases the
+  size of the binary.
+- Internal crates have been "folded" in with the main code. This should
+  hopefully make editing the code a bit simpler.