v0.16.0 - Van vleck, msrv 1.65, mwalib 1.8.2, marlu 0.15

Van Vleck corrections
* msrv 1.65, mwalib 1.8.2, marlu 0.15, ndarray 0.16, fitsio0.21.6
* don't correct flagged ants. comment out cheby corrections
* tests comparing with pyuvdata
* read bscale from mwalib
MWATelescope/mwalib#85
* stop iterating for sigma < 0.5
* --no-geom conflicts with --pointing-centre and --phase-centre
* warnings for bad kappa
* error message on non-legacy obs
* fix macos ci install deps

Author: d3v-null

.github/workflows/macos_ci.yml

@@ -33,14 +33,23 @@ jobs:
         uses: davidB/rust-cargo-make@v1
       - name: Install Dependencies
         run: |
-          # cargo make install_deps # doesn't work
-          brew install casacore/tap/casacore mwatelescope/tap/aoflagger
+          # cargo make install_deps
+          # doesn't work on macos, brew install ... says you need arch -arm64 brew ...
+          # but there's no way to distinguish between macos-13 and macos-14
+          # using uname -m or arch
+          # https://github.com/actions/runner-images/issues/9471#issuecomment-1992603303
+          for f in $(find /usr/local/bin -type l -print); do \
+            (readlink $f | grep -q -s "/Library") && echo Removing "$f" && rm -f "$f"; \
+          done
+          INSTALL="brew install"
+          [ "${{ matrix.os }}" == "macos-14" ] && INSTALL="arch -arm64 brew install"
+          $INSTALL mwatelescope/tap/aoflagger
+          echo "DYLD_FALLBACK_LIBRARY_PATH=$(brew --prefix)/lib/" >> $GITHUB_ENV
+          echo "AOFLAGGER_LIB=$(brew --prefix)/lib/" >> $GITHUB_ENV
+          echo "AOFLAGGER_INCLUDE_DIR=$(brew --prefix)/include/" >> $GITHUB_ENV
+          echo "PKG_CONFIG_PATH=$(brew --prefix)/lib/pkgconfig/" >> $GITHUB_ENV
       - name: Run tests
         run: |
           cargo make test_no_default
           cargo make test_no_flag
           cargo make test
-        env:
-          DYLD_FALLBACK_LIBRARY_PATH: /opt/homebrew/lib/
-          AOFLAGGER_LIB: /opt/homebrew/lib/
-          AOFLAGGER_INCLUDE_DIR: /opt/homebrew/include/

Cargo.lock

@@ -1,7 +1,7 @@
 [package]
 name = "birli"
 description = "A preprocessing pipeline for the Murchison Widefield Array"
-version = "0.15.1"
+version = "0.16.0"
 readme = "README.md"
 homepage = "https://github.com/MWATelescope/Birli"
 repository = "https://github.com/MWATelescope/Birli"
@@ -12,7 +12,7 @@ authors = [
     "Luke A. Williams <luke.a.williams@curtin.edu.au>",
 ]
 edition = "2021"
-rust-version = "1.64"
+rust-version = "1.65"
 license = "MPL-2.0"
 keywords = ["radioastronomy", "mwa", "astronomy", "aoflagger", "cotter"]
 categories = ["science", "parsing"]
@@ -43,9 +43,11 @@ indicatif = { version = "0.17.0", features = ["rayon"] }
 itertools = "0.10.0"
 lazy_static = "1.4.0"
 log = "0.4.0"
-marlu = "0.14.0"
+marlu = "0.15.0"
 regex = "1.4.0"
 thiserror = "1.0.0"
+errorfunctions = "0.2.0"
+serde-pickle = "1.1.1"
 
 # aoflagger feature
 aoflagger_sys = { version = "0.1.2", optional = true }
@@ -64,7 +66,7 @@ csv = "1.1"
 float-cmp = "0.9"
 glob = "0.3"
 lexical = "6.0"
-marlu = { version = "0.14.0", features = ["approx"] }
+marlu = { version = "0.15.0", features = ["approx"] }
 ndarray = { version = "0.16.0", features = ["approx"] }
 tempfile = "3.3"
 
@@ -91,6 +93,10 @@ opt-level = 3
 
 [patch.crates-io]
 # marlu = { path = "../Marlu" }
-# marlu = { git = "https://github.com/MWATelescope/Marlu", branch = "birli-150" }
+# marlu = { git = "https://github.com/MWATelescope/Marlu", branch = "mwalib-1.8.0" }
 # mwalib = { path = "../mwalib" }
-# mwalib = { git = "https://github.com/MWATelescope/mwalib", branch = "digital_gains_plus" }
+# mwalib = { git = "https://github.com/MWATelescope/mwalib", branch = "pyo3_stub_chrono_fix" }
+# aoflagger_sys = { git = "https://github.com/MWATelescope/rust-aoflagger", branch = "sonoma-fix" }
+
+# TODO: update to cxx 1.0.129 when MSRV >= 1.67
+url = { git = "https://github.com/servo/rust-url", tag = "v2.5.2" }

Cargo.toml

@@ -124,7 +124,13 @@ dependencies = ["linux_install_aoflagger"]
 
 [tasks.mac_install_deps]
 script = """
-brew install casacore/tap/casacore mwatelescope/tap/aoflagger
+INSTALL="brew install"
+# in github actions runners:
+# - macos-13: uname -m => x86_64, arch => i386
+# - macos-14: uname -m => x86_64, arch => i386
+# but macos-14 should be arm64 ?
+# in that case, we want INSTALL="arch -arm64 $INSTALL" apparently?
+$INSTALL mwatelescope/tap/aoflagger
 """
 
 [tasks.install_deps]
@@ -200,6 +206,10 @@ args = ["test", "--no-default-features", "--release"]
 command = "cargo"
 args = ["test", "--no-default-features", "--release", "--features=cli"]
 
+[tasks.test_package]
+command = "cargo"
+args = ["package", "--allow-dirty"]
+
 [tasks.ci]
 dependencies = [
   "clean",
@@ -219,4 +229,5 @@ dependencies = [
   "test_no_default",
   "test",
   "rustdoc",
+  "test_package",
 ]