Convert to a monorepo (#338)

* start migrating to monorepo

* bring over psqs, start modifying tests to work on multiple threads

* nightly clippy, fix dependencies, and get compiling

* update installation recipe and regenerate man page

* convert psqs to mod.rs

* delete psqs main??

* use workspace psqs

* copy over psqs readme, minus badges

* copy symm and run clippy

tests are failing because of mixed Molecule types, so I'll have to move intder
and spectro too before running tests again

* copy over intder, spectro, and spectro-bin

* clippy

* copy taylor

* pbqff uses include-ignored, so mark this as not a test

* copy over anpass and rename, use faster test profile

because the profile must be in the project root

* add note about tensor

* delete nightly-only benchmarks

* filter out polyads caused by workspace --all-features in test ci

* use `get` to avoid oob, warn on errors

this is obviously a dirty hack but I'm not interested in actually fixing polyads
right now

Cargo.toml

@@ -1,33 +1,42 @@
-[package]
-name = "pbqff"
-version = "0.1.0"
+[workspace]
+members = ["crates/*"]
+resolver = "2"
+
+[workspace.package]
 edition = "2021"
 
-[dependencies]
-intder = { git = "https://github.com/ntBre/intder" }
-psqs = { git = "https://github.com/ntBre/psqs" }
-rust-anpass = { git = "https://github.com/ntBre/rust-anpass" }
-spectro = { git = "https://github.com/ntBre/spectro" }
-symm = { git = "https://github.com/ntBre/symm" }
-taylor = { git = "https://github.com/ntBre/taylor" }
+[workspace.dependencies]
+anpass = { path = "crates/anpass" }
+psqs = { path = "crates/psqs" }
+symm = { path = "crates/symm" }
+intder = { path = "crates/intder" }
+spectro = { path = "crates/spectro" }
+taylor = { path = "crates/taylor" }
+
+# not really interested in bringing this one over. it's the least-used and
+# least-changing, and I should probably just replace its usage with ndarray
+# anyway
+tensor = { git = "https://github.com/ntBre/tensor" }
 
+approx = "0.5.1"
+assert_cmd = "2.0.16"
+chrono = "0.4.23"
 clap = { version = "4.5.23", features = ["derive"] }
+criterion = "0.5.0"
 env_logger = "0.11.3"
+insta = { version = "1.41.1", features = ["filters"] }
 libc = "0.2.169"
 log = "0.4.22"
 nalgebra = "0.33.2"
+ndarray = { version = "0.15.6", features = ["approx-0_5"] }
+rayon = "1.5.3"
+regex = { version = "1.9.1" }
 rustc-hash = "2.1.0"
 serde = { version = "1.0", features = ["derive"] }
 serde_json = "1.0"
-toml = "0.8.10"
-
-[dev-dependencies]
-approx = "0.5.1"
-assert_cmd = "2.0.16"
-insta = { version = "1.41.1", features = ["filters"] }
 tempfile = "3.14.0"
 test-case = "3.3.1"
+toml = "0.8.10"
 
-[[bin]]
-name = "cart"
-path = "src/bin/cart.rs"
+[profile.test]
+opt-level = 3  # mostly for anpass

Makefile

@@ -13,7 +13,7 @@ clean:
 	cargo clean
 
 clippy:
-	cargo clippy --all-features --all-targets --workspace
+	cargo +nightly clippy --all-features --all-targets --workspace
 
 cover:
 	cargo tarpaulin --color=never --skip-clean ${TESTFLAGS} ${ARGS}
@@ -43,7 +43,7 @@ endif
 install:
 	cargo install --path . --bin pbqff
 
-src := build.rs $(shell find src -name '*.rs')
+src := $(shell find . -name '*.rs')
 
 target/release/pbqff: $(src)
 	cargo build --release
@@ -83,10 +83,11 @@ docs: man/rpbqff.1
 %.pdf: %.1
 	groff -Tpdf $? -mman > $@
 
-man/config.man: src/config.rs scripts/config.awk
+pbqff := crates/pbqff
+man/config.man: $(pbqff)/src/config.rs scripts/config.awk
 	scripts/config.awk $< > $@
 
-man/rpbqff.1: man/rpbqff.head man/config.man man/example.man testfiles/test.toml man/rpbqff.tail
+man/rpbqff.1: man/rpbqff.head man/config.man man/example.man $(pbqff)/testfiles/test.toml man/rpbqff.tail
 	cat $^ > $@
 
 scripts: qffbuddy/qffbuddy*

crates/anpass/Cargo.toml

@@ -0,0 +1,11 @@
+[package]
+name = "anpass"
+version = "0.1.0"
+edition = "2021"
+
+[dependencies]
+regex = { workspace = true }
+nalgebra = { workspace = true }
+
+[dev-dependencies]
+approx = { workspace = true }

crates/anpass/README.md

@@ -0,0 +1,2 @@
+# anpass
+ordinary least-squares fitting and stationary point determination