From 0fa8071a128a148861b7082b2198c044d005f178 Mon Sep 17 00:00:00 2001
From: Jack Huey <31162821+jackh726@users.noreply.github.com>
Date: Mon, 29 Jan 2024 11:41:35 -0500
Subject: [PATCH] Update some things

---
 .github/workflows/release.yml  | 13 +++++++++++--
 .travis.yml                    |  9 ---------
 LICENSE                        |  2 +-
 Dockerfile => bench/Dockerfile |  6 ++++--
 bench/bench_plots.ipynb        | 11 ++++++++---
 pybigtools/LICENSE             | 21 ---------------------
 6 files changed, 24 insertions(+), 38 deletions(-)
 delete mode 100644 .travis.yml
 rename Dockerfile => bench/Dockerfile (86%)
 delete mode 100644 pybigtools/LICENSE

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 95f03f5..051c0fd 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -17,6 +17,14 @@ jobs:
             target: x86_64-unknown-linux-gnu
             asset_name: bigtools-linux-gnu
             remote: true
+          - os: windows-msvc-latest
+            target: x86_64-pc-windows-msvc
+            asset_name: bigtools-windows-msvc
+            remote: true
+          - os: macos-latest
+            target: x86_64-apple-darwin
+            asset_name: bigtools-apple-darwin
+            remote: true
     steps:
       - name: Checkout code
         uses: actions/checkout@v2
@@ -30,6 +38,8 @@ jobs:
           files: |
             target/release/bedgraphtobigwig;
             target/release/bedtobigbed;
+            target/release/bigbedinfo;
+            target/release/bigbedtobed;
             target/release/bigtools;
             target/release/bigwigaverageoverbed;
             target/release/bigwiginfo;
@@ -37,9 +47,8 @@ jobs:
             target/release/bigwigtobedgraph;
             target/release/bigwigvaluesoverbed
           dest: ${{ matrix.asset_name }}.zip
-      - name: Asset upload
+      - name: Zip upload
         uses: shogo82148/actions-upload-release-asset@v1
         with:
           upload_url: ${{ github.event.release.upload_url }}
           asset_path: ${{ github.workspace }}/${{ matrix.asset_name }}.zip
-
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 9b46883..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-language: rust
-rust:
-#  - stable
-#  - beta
-  - nightly
-#jobs:
-#  allow_failures:
-#    - rust: nightly
-#  fast_finish: true
diff --git a/LICENSE b/LICENSE
index 6b517a6..a677ea2 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2023 Jack Huey
+Copyright (c) 2024 Jack Huey
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
diff --git a/Dockerfile b/bench/Dockerfile
similarity index 86%
rename from Dockerfile
rename to bench/Dockerfile
index 218fc5c..1dc73ed 100644
--- a/Dockerfile
+++ b/bench/Dockerfile
@@ -1,8 +1,10 @@
+# Note: this should be build from the parent directory
+
 FROM rust:buster as build
 
 RUN mkdir /bigtools
-COPY ./src /bigtools/src
-COPY ./Cargo.toml /bigtools
+COPY ./bigtools/src /bigtools/src
+COPY ./bigtools/Cargo.toml /bigtools
 COPY ./Cargo.lock /bigtools
 RUN cd /bigtools && cargo install --path .
 
diff --git a/bench/bench_plots.ipynb b/bench/bench_plots.ipynb
index 1e4722a..f269b01 100644
--- a/bench/bench_plots.ipynb
+++ b/bench/bench_plots.ipynb
@@ -298,7 +298,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "plotting",
+   "display_name": "Python 3.11.4 ('bigtools')",
    "language": "python",
    "name": "python3"
   },
@@ -312,9 +312,14 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.11.4"
   },
-  "orig_nbformat": 4
+  "orig_nbformat": 4,
+  "vscode": {
+   "interpreter": {
+    "hash": "4e8d9598e99a1b5bc615fc1811f6f41b50fc824837143c71885b70d1ca899c99"
+   }
+  }
  },
  "nbformat": 4,
  "nbformat_minor": 2
diff --git a/pybigtools/LICENSE b/pybigtools/LICENSE
deleted file mode 100644
index 6b517a6..0000000
--- a/pybigtools/LICENSE
+++ /dev/null
@@ -1,21 +0,0 @@
-MIT License
-
-Copyright (c) 2023 Jack Huey
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.