ci: create workflows and do some housekeeping (#154)

Adds a CI pipeline along with some quality-of-life improvements such as an editorconfig, Makefile, functional tests refinements, dependency updates, and fixes suggested by `clippy` and `rustfmt`.

Closes #108, #80

.codespellrc

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+[codespell]
+skip = .git,target,Cargo.toml,Cargo.lock,mutants*
+ignore-words-list = crate,ser

.config/mutants.toml

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+test_tool = "nextest"

.config/nextest.toml

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+[store]
+# The directory under the workspace root at which nextest-related files are
+# written. Profile-specific storage is currently written to dir/<profile-name>.
+dir = "target/nextest"
+
+# This section defines the default nextest profile. Custom profiles are layered
+# on top of the default profile.
+[profile.default]
+# "retries" defines the number of times a test should be retried. If set to a
+# non-zero value, tests that succeed on a subsequent attempt will be marked as
+# flaky. Can be overridden through the `--retries` option.
+# Examples
+# * retries = 3
+# * retries = { backoff = "fixed", count = 2, delay = "1s" }
+retries = { backoff = "exponential", count = 3, delay = "1s", jitter = true, max-delay = "10s" }
+
+# The number of threads to run tests with. Supported values are either an integer or
+# the string "num-cpus". Can be overridden through the `--test-threads` option.
+test-threads = "num-cpus"
+
+# The number of threads required for each test. This is generally used in overrides to
+# mark certain tests as heavier than others. However, it can also be set as a global parameter.
+threads-required = 1
+
+# Show these test statuses in the output.
+#
+# The possible values this can take are:
+# * none: no output
+# * fail: show failed (including exec-failed) tests
+# * retry: show flaky and retried tests
+# * slow: show slow tests
+# * pass: show passed tests
+# * skip: show skipped tests (most useful for CI)
+# * all: all of the above
+#
+# Each value includes all the values above it; for example, "slow" includes
+# failed and retried tests.
+#
+# Can be overridden through the `--status-level` flag.
+status-level = "all"
+
+# Similar to status-level, show these test statuses at the end of the run.
+final-status-level = "flaky"
+
+# "failure-output" defines when standard output and standard error for failing tests are produced.
+# Accepted values are
+# * "immediate": output failures as soon as they happen
+# * "final": output failures at the end of the test run
+# * "immediate-final": output failures as soon as they happen and at the end of
+#   the test run; combination of "immediate" and "final"
+# * "never": don't output failures at all
+#
+# For large test suites and CI it is generally useful to use "immediate-final".
+#
+# Can be overridden through the `--failure-output` option.
+failure-output = "immediate"
+
+# "success-output" controls production of standard output and standard error on success. This should
+# generally be set to "never".
+success-output = "never"
+
+# Cancel the test run on the first failure. For CI runs, consider setting this
+# to false.
+fail-fast = true
+
+# Treat a test that takes longer than the configured 'period' as slow, and print a message.
+# See <https://nexte.st/book/slow-tests> for more information.
+#
+# Optional: specify the parameter 'terminate-after' with a non-zero integer,
+# which will cause slow tests to be terminated after the specified number of
+# periods have passed.
+# Example: slow-timeout = { period = "60s", terminate-after = 2 }
+slow-timeout = { period = "60s" }
+
+# Treat a test as leaky if after the process is shut down, standard output and standard error
+# aren't closed within this duration.
+#
+# This usually happens in case of a test that creates a child process and lets it inherit those
+# handles, but doesn't clean the child process up (especially when it fails).
+#
+# See <https://nexte.st/book/leaky-tests> for more information.
+leak-timeout = "100ms"
+
+# `nextest archive` automatically includes any build output required by a standard build.
+# However sometimes extra non-standard files are required.
+# To address this, "archive.include" specifies additional paths that will be included in the archive.
+archive.include = [
+  # Examples:
+  #
+  # { path = "application-data", relative-to = "target" },
+  # { path = "data-from-some-dependency/file.txt", relative-to = "target" },
+  #
+  # In the above example:
+  # * the directory and its contents at "target/application-data" will be included recursively in the archive.
+  # * the file "target/data-from-some-dependency/file.txt" will be included in the archive.
+]
+
+[profile.default.junit]
+# Output a JUnit report into the given file inside 'store.dir/<profile-name>'.
+# If unspecified, JUnit is not written out.
+
+path = "junit.xml"
+
+# The name of the top-level "report" element in JUnit report. If aggregating
+# reports across different test runs, it may be useful to provide separate names
+# for each report.
+report-name = "nextest-run"
+
+# Whether standard output and standard error for passing tests should be stored in the JUnit report.
+# Output is stored in the <system-out> and <system-err> elements of the <testcase> element.
+store-success-output = false
+
+# Whether standard output and standard error for failing tests should be stored in the JUnit report.
+# Output is stored in the <system-out> and <system-err> elements of the <testcase> element.
+#
+# Note that if a description can be extracted from the output, it is always stored in the
+# <description> element.
+store-failure-output = true
+
+# This profile is activated if MIRI_SYSROOT is set.
+[profile.default-miri]
+
+# This profile is used in CI (use with `--profile ci`)
+[profile.ci]
+# Print out output for failing tests as soon as they fail, and also at the end
+# of the run (for easy scrollability).
+failure-output = "immediate-final"
+# Do not cancel the test run on the first failure.
+fail-fast = false
+
+[profile.ci.junit]
+path = "junit.xml"
+report-name = "nextest-run-ci"
+store-success-output = true
+store-failure-output = true

.editorconfig

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+# EditorConfig helps developers define and maintain consistent
+# coding styles between different editors and IDEs
+# editorconfig.org
+
+root = true
+
+[*]
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+indent_style = space
+indent_size = 4
+
+[*.rs]
+max_line_length = 100
+
+[*.{yml,yaml,toml}]
+indent_size = 2
+
+[*.md]
+# double whitespace at end of line
+# denotes a line break in Markdown
+trim_trailing_whitespace = false
+
+[Makefile]
+indent_style = tab
+
+[]

.github/PULL_REQUEST_TEMPLATE.md

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+## Description
+
+<!--
+Provide a brief summary of the changes and the motivation behind them.
+-->
+
+### Type of Change
+
+<!--
+Select the type of change your PR introduces (put an `x` in all that apply):-
+-->
+
+-   [ ] Bug fix (non-breaking change which fixes an issue)
+-   [ ] New feature/Enhancement (non-breaking change which adds functionality or enhances an existing one)
+-   [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+-   [ ] Documentation update
+-   [ ] Refactor
+
+## Checklist
+
+<!--
+Ensure all the following are checked:
+-->
+
+-   [ ] I have performed a self-review of my code.
+-   [ ] I have commented my code where necessary.
+-   [ ] I have updated the documentation if needed.
+-   [ ] My changes do not introduce new warnings.
+-   [ ] I have added tests that prove my changes are effective or that my feature works.
+-   [ ] New and existing tests pass with my changes.
+
+## Related Issues
+
+<!--
+Link any related issues (e.g., `closes #123`, `fixes #456`).
+-->

.github/dependabot.yml

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+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+  - package-ecosystem: "pip"
+    directory: "test/"
+    schedule:
+      interval: "monthly"

.github/workflows/dependencies.yml

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+# Runs `cargo update` periodically.
+
+name: Update Dependencies
+
+on:
+  schedule:
+    # Run at the first of every month
+    - cron: "0 0 1 * *"
+  workflow_dispatch:
+    # Needed so we can run it manually
+
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  BRANCH: cargo-update
+  TITLE: "chore(deps): monthly `cargo update`"
+  BODY: |
+    Automation to keep dependencies in `Cargo.lock` current.
+
+    <details><summary><strong>cargo update log</strong></summary>
+    <p>
+
+    ```log
+    $cargo_update_log
+    ```
+
+    </p>
+    </details>
+
+jobs:
+  update:
+    name: Update
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: dtolnay/rust-toolchain@nightly
+
+      - name: cargo update
+        # Remove first line that always just says "Updating crates.io index"
+        run: cargo update --color never 2>&1 | sed '/crates.io index/d' | tee -a cargo_update.log
+
+      - name: craft commit message and PR body
+        id: msg
+        run: |
+          export cargo_update_log="$(cat cargo_update.log)"
+
+          echo "commit_message<<EOF" >> $GITHUB_OUTPUT
+          printf "$TITLE\n\n$cargo_update_log\n" >> $GITHUB_OUTPUT
+          echo "EOF" >> $GITHUB_OUTPUT
+
+          echo "body<<EOF" >> $GITHUB_OUTPUT
+          echo "$BODY" | envsubst >> $GITHUB_OUTPUT
+          echo "EOF" >> $GITHUB_OUTPUT
+
+      - name: Create Pull Request
+        uses: peter-evans/create-pull-request@v6
+        with:
+          add-paths: ./Cargo.lock
+          commit-message: ${{ steps.msg.outputs.commit_message }}
+          title: ${{ env.TITLE }}
+          body: ${{ steps.msg.outputs.body }}
+          branch: ${{ env.BRANCH }}

.github/workflows/docs.yml

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+name: Docs
+
+on:
+  push:
+    branches: [master]
+
+env:
+  CARGO_TERM_COLOR: always
+
+jobs:
+  docs:
+    name: Generate docs
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    steps:
+      - uses: actions/checkout@v4
+      - uses: dtolnay/rust-toolchain@nightly
+      - uses: Swatinem/rust-cache@v2
+        with:
+          cache-on-failure: true
+      - run: cargo doc --document-private-items
+        env:
+          RUSTDOCFLAGS: --show-type-layout --enable-index-page -Zunstable-options -D warnings
+      - name: Compress docs artifacts
+        run: tar czf vertex-core-docs.tar.gz target/doc
+      - name: Archive docs
+        uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: docs
+          path: vertex-core-docs.tar.gz

.github/workflows/functional.yml

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+name: Run functional tests
+
+on:
+  pull_request:
+  merge_group:
+  push:
+    branches: [master]
+
+env:
+  CARGO_TERM_COLOR: always
+
+jobs:
+  run-functional-tests:
+    name: Run functional tests
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "^3.10" # Keep in sync with `pyproject.toml`
+
+      - name: Install Poetry
+        run: |
+          curl -sSL https://install.python-poetry.org | python -
+          echo "${HOME}/.local/bin" >> $GITHUB_PATH
+
+      - name: Configure Poetry to create the virtual environment inside the project
+        run: poetry config virtualenvs.in-project true
+
+      - name: Install python dependencies
+        run: cd functional-tests && poetry install --no-root && cd -
+
+      - name: Set up Rust
+        uses: dtolnay/rust-toolchain@nightly
+      - uses: Swatinem/rust-cache@v2
+        with:
+          cache-on-failure: true
+
+      - name: Build Cargo project
+        run: cargo build
+
+      - name: Install bitcoind
+        run: |
+          wget https://bitcoin.org/bin/bitcoin-core-27.0/bitcoin-27.0-x86_64-linux-gnu.tar.gz
+          tar xzf bitcoin-27.0-x86_64-linux-gnu.tar.gz
+          sudo install -m 0755 -t /usr/local/bin bitcoin-27.0/bin/*
+          bitcoind --version
+
+      - name: Run functional tests (1)
+        id: funcTestsRun1
+        continue-on-error: true
+        run: |
+          export PATH=$(realpath target/debug/):$PATH
+          which alpen-vertex-sequencer
+          cd functional-tests && \
+          poetry run python entry.py
+
+      # Run again just to be sure as some tests are flaky
+      - name: Run functional tests (2)
+        if: steps.funcTestsRun1.outcome == 'failure'
+        run: |
+          export PATH=$(realpath target/debug/):$PATH
+          which alpen-vertex-sequencer
+          cd functional-tests && \
+          poetry run python entry.py