From 5d559b764e9fb1304f94ee06e22d5c381452213e Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Tue, 7 May 2024 07:15:05 +0200 Subject: [PATCH 01/14] switch to dtolnay/rust-toolchain --- .github/workflows/build-test.yml | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml index 7c3a4a7e..3b99bb1f 100644 --- a/.github/workflows/build-test.yml +++ b/.github/workflows/build-test.yml @@ -12,17 +12,14 @@ jobs: fetch-depth: 0 - name: Install latest stable rust - uses: actions-rs/toolchain@v1 + uses: dtolnay/rust-toolchain@stable with: toolchain: stable override: true components: rustfmt, clippy - name: Run cargo fmt - uses: actions-rs/cargo@v1 - with: - command: fmt - args: --all -- --check + run: cargo fmt --all -- --check --verbose --message-format=human - name: cache rust uses: Swatinem/rust-cache@v2 From 13298f1c163140d0cb0e1ed195a2429358d9f94f Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Tue, 7 May 2024 07:18:45 +0200 Subject: [PATCH 02/14] remove --message-format --- .github/workflows/build-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml index 3b99bb1f..f3b38f13 100644 --- a/.github/workflows/build-test.yml +++ b/.github/workflows/build-test.yml @@ -19,7 +19,7 @@ jobs: components: rustfmt, clippy - name: Run cargo fmt - run: cargo fmt --all -- --check --verbose --message-format=human + run: cargo fmt --all -- --check --verbose - name: cache rust uses: Swatinem/rust-cache@v2 From d4ab1ebdd66428a2b857fd2b6bdb23289f3d0762 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Tue, 7 May 2024 07:38:46 +0200 Subject: [PATCH 03/14] try commenting out lto param in profile.release --- Cargo.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cargo.toml b/Cargo.toml index af09c331..0c3c601e 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -35,5 +35,5 @@ tempfile = "3.10.0" [profile.release] #target-cpu=native -lto = "thin" +#lto = "thin" opt-level = 3 From 049f63489c7d8e2826e14f28f3a15969d89cab14 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Tue, 7 May 2024 08:25:43 +0200 Subject: [PATCH 04/14] try adding a few conda packages to build env --- .github/workflows/build-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml index f3b38f13..8c2b3ea8 100644 --- a/.github/workflows/build-test.yml +++ b/.github/workflows/build-test.yml @@ -49,7 +49,7 @@ jobs: - name: install dependencies shell: bash -l {0} - run: mamba install git compilers maturin pytest pandas + run: mamba install git compilers maturin pytest pandas crossenv libclang clangdev - name: build shell: bash -l {0} From 82806a3dcddeb3f65f3a005af6a329463a86e8b0 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Thu, 9 May 2024 04:22:04 -0700 Subject: [PATCH 05/14] try installing rust via conda --- .github/workflows/build-test.yml | 21 +++++++-------------- 1 file changed, 7 insertions(+), 14 deletions(-) diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml index 8c2b3ea8..86405781 100644 --- a/.github/workflows/build-test.yml +++ b/.github/workflows/build-test.yml @@ -11,19 +11,6 @@ jobs: with: fetch-depth: 0 - - name: Install latest stable rust - uses: dtolnay/rust-toolchain@stable - with: - toolchain: stable - override: true - components: rustfmt, clippy - - - name: Run cargo fmt - run: cargo fmt --all -- --check --verbose - - - name: cache rust - uses: Swatinem/rust-cache@v2 - - name: cache conda uses: actions/cache@v4 env: @@ -33,6 +20,9 @@ jobs: key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }} + - name: cache rust + uses: Swatinem/rust-cache@v2 + - name: setup conda uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca with: @@ -49,7 +39,10 @@ jobs: - name: install dependencies shell: bash -l {0} - run: mamba install git compilers maturin pytest pandas crossenv libclang clangdev + run: mamba install git compilers maturin pytest pandas rust + + - name: Run cargo fmt + run: cargo fmt --all -- --check --verbose - name: build shell: bash -l {0} From a4d741282eec8dfbb6b62da79f083a074cffdc76 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Thu, 9 May 2024 04:33:04 -0700 Subject: [PATCH 06/14] add optional features to env_logger for anstream --- Cargo.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cargo.toml b/Cargo.toml index 1be711e5..65daa892 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -16,7 +16,7 @@ sourmash = { version = "0.13.1", features = ["branchwater"] } serde_json = "1.0.116" niffler = "2.4.0" log = "0.4.14" -env_logger = "0.11.3" +env_logger = { version = "0.11.3", optional = true } simple-error = "0.3.0" anyhow = "1.0.82" zip = { version = "0.6", default-features = false, features = ["deflate"] } From c37830d84a43ec76b7bad77a7af7f9c15f88d90a Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Thu, 9 May 2024 04:40:57 -0700 Subject: [PATCH 07/14] pin rust version --- .github/workflows/build-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml index 86405781..e445a596 100644 --- a/.github/workflows/build-test.yml +++ b/.github/workflows/build-test.yml @@ -39,7 +39,7 @@ jobs: - name: install dependencies shell: bash -l {0} - run: mamba install git compilers maturin pytest pandas rust + run: mamba install git compilers maturin pytest pandas rust==1.75.0 - name: Run cargo fmt run: cargo fmt --all -- --check --verbose From 95a0a27cf4f64d1d2e1f7bcf02d15502cf11f3fe Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Thu, 9 May 2024 04:48:46 -0700 Subject: [PATCH 08/14] try using latest setup-miniconda --- .github/workflows/build-test.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml index e445a596..1a01c02f 100644 --- a/.github/workflows/build-test.yml +++ b/.github/workflows/build-test.yml @@ -24,10 +24,10 @@ jobs: uses: Swatinem/rust-cache@v2 - name: setup conda - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca + uses: conda-incubator/setup-miniconda@3 with: auto-update-conda: true - python-version: 3.11 + python-version: 3.12 channels: conda-forge,bioconda miniforge-variant: Mambaforge miniforge-version: latest From 34b1af2e022cb7ecd19780102b02dcb1217df277 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Thu, 9 May 2024 04:51:19 -0700 Subject: [PATCH 09/14] fix v --- .github/workflows/build-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml index 1a01c02f..da3755fb 100644 --- a/.github/workflows/build-test.yml +++ b/.github/workflows/build-test.yml @@ -24,7 +24,7 @@ jobs: uses: Swatinem/rust-cache@v2 - name: setup conda - uses: conda-incubator/setup-miniconda@3 + uses: conda-incubator/setup-miniconda@v3 with: auto-update-conda: true python-version: 3.12 From 89eb9652c8fd51f3c062f7b48b20c340aaf86aff Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Thu, 9 May 2024 04:56:28 -0700 Subject: [PATCH 10/14] wtf --- .github/workflows/build-test.yml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml index da3755fb..e7850632 100644 --- a/.github/workflows/build-test.yml +++ b/.github/workflows/build-test.yml @@ -39,7 +39,11 @@ jobs: - name: install dependencies shell: bash -l {0} - run: mamba install git compilers maturin pytest pandas rust==1.75.0 + run: mamba install rust==1.75.0 + + - name: install dependencies 2 + shell: bash -l {0} + run: mamba install compilers maturin pytest pandas - name: Run cargo fmt run: cargo fmt --all -- --check --verbose From 519ae4b3a11f16ac74443c0258a8b42c7899551c Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Thu, 9 May 2024 05:05:48 -0700 Subject: [PATCH 11/14] Wtf --- .github/workflows/build-test.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml index e7850632..4640b46b 100644 --- a/.github/workflows/build-test.yml +++ b/.github/workflows/build-test.yml @@ -37,6 +37,12 @@ jobs: auto-activate-base: false use-only-tar-bz2: true + - run: conda info + - run: conda list + - run: conda config --show + + - run: mamba search rust + - name: install dependencies shell: bash -l {0} run: mamba install rust==1.75.0 From e368bd37afb3dc85cd3629eeb4c3bbdc5b4701a0 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Thu, 9 May 2024 05:15:21 -0700 Subject: [PATCH 12/14] stuff cache? --- .github/workflows/build-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml index 4640b46b..c556b452 100644 --- a/.github/workflows/build-test.yml +++ b/.github/workflows/build-test.yml @@ -14,7 +14,7 @@ jobs: - name: cache conda uses: actions/cache@v4 env: - CACHE_NUMBER: 0 + CACHE_NUMBER: 1 with: path: ~/conda_pkgs_dir key: From 0512dedce159f79b017df66e24b1ee44ee40e353 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Thu, 9 May 2024 05:24:12 -0700 Subject: [PATCH 13/14] why not --- .github/workflows/build-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml index c556b452..54742ffa 100644 --- a/.github/workflows/build-test.yml +++ b/.github/workflows/build-test.yml @@ -35,7 +35,7 @@ jobs: mamba-version: "*" activate-environment: sourmash_dev auto-activate-base: false - use-only-tar-bz2: true +# use-only-tar-bz2: true - run: conda info - run: conda list From bca9d90baf9ce8a79d0a18ddc98453d10fce90ad Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Thu, 9 May 2024 05:37:27 -0700 Subject: [PATCH 14/14] test build again, w/cache