Feature/upgrade deps 09 22 (#13)

* fix katex to display inline math and math blocks

* upgrade snafu dependency

* upgrade levmar and nalgebra dependencies as much as possible

* fmt

* latest fmt, clippy

* bump version

* Try fix broken coverage report

.github/workflows/coverage.yml

@@ -27,11 +27,11 @@ jobs:
       - name: Run cargo-tarpaulin
         uses: actions-rs/tarpaulin@v0.1
         with:
-          version: '0.15.0'
+          #version: '0.15.0'
           args: '-- --test-threads 1'
 
       - name: Upload to codecov.io
-        uses: codecov/codecov-action@v1.0.2
+        uses: codecov/codecov-action@v3
         with:
           token: ${{secrets.CODECOV_TOKEN}}
 

Cargo.toml

@@ -1,8 +1,8 @@
 [package]
 name = "varpro"
-version = "0.3.0"
+version = "0.4.0"
 authors = ["geo-ant"]
-edition = "2018"
+edition = "2021"
 license = "MIT"
 homepage = "https://github.com/geo-ant/varpro"
 repository = "https://github.com/geo-ant/varpro"
@@ -14,9 +14,9 @@ keywords = ["nonlinear","least","squares","fitting","regression"]
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
 [dependencies]
-snafu = "0.6"
-levenberg-marquardt = "0.11"
-nalgebra = "0.29"
+snafu = "0.7"
+levenberg-marquardt = "0.12"
+nalgebra = "0.30"
 num-traits = "0.2"
 
 [dev-dependencies]
@@ -25,4 +25,4 @@ approx = "0.5"
 [package.metadata.docs.rs]
 # To build locally use
 #   RUSTDOCFLAGS="--html-in-header katex-header.html" cargo doc --no-deps --open
-rustdoc-args = [ "--html-in-header", "katex-header.html" ]
+rustdoc-args = [ "--html-in-header", "katex-header.html" ]

katex-header.html

@@ -4,49 +4,49 @@
 .katex { font-size: 1.07em; }
 </style>
 <script>
-  "use strict";
-  document.addEventListener("DOMContentLoaded", function () {
-    // display blocks
-    document.querySelectorAll('pre > code.language-math').forEach((el) => {
-      let p = document.createElement("p");
-      katex.render(el.innerText, p, {displayMode: true, throwOnError: false});
-      el.parentNode.parentNode.replaceChild(p, el.parentNode);
-    });
+    "use strict";
+    document.addEventListener("DOMContentLoaded", function () {
+              var maths = document.getElementsByClassName("language-math");
+              for (var i=0; i<maths.length; i++) {
+                            var el = maths[i];
+                            katex.render(el.innerText, el, {displayMode: true});
+
+              }
 
-    // inline blocks
-    document.querySelectorAll(':not(pre) > code').forEach((el) => {
-      let text = el.innerText;
-      if (!text.startsWith('$') || !text.endsWith('$')) {
-        return;
-      }
-      let span = document.createElement("span");
-      katex.render(text.substr(1, text.length - 2), span, {displayMode: false, throwOnError: false});
-      el.parentNode.replaceChild(span, el);
-    });
+            // inline blocks
+            document.querySelectorAll(':not(pre) > code').forEach((el) => {
+                      let text = el.innerText;
+                      if (!text.startsWith('$') || !text.endsWith('$')) {
+                                  return;
+                                }
+                      let span = document.createElement("span");
+                      katex.render(text.substr(1, text.length - 2), span, {displayMode: false, throwOnError: false});
+                      el.parentNode.replaceChild(span, el);
+                    });
 
-    // comment in code
-    document.querySelectorAll('pre span.comment').forEach((el) => {
-      let html = el.innerText;
-      let children = [];
-      let offset = 0;
-      [...html.matchAll(/(?:[^\$]|^)(\$(?:\\.|[^\$])+\$)(?!\$)/g)].forEach((match) => {
-        let textBefore = html.substring(offset, match.index + 1);
-        children.push(document.createTextNode(textBefore));
-        let math = match[1].substring(1, match[1].length - 1);
-        let span = document.createElement("span");
-        katex.render(math, span, {displayMode: false, throwOnError: false});
-        children.push(span);
-        offset = match.index + match[0].length;
+            // comment in code
+            document.querySelectorAll('pre span.comment').forEach((el) => {
+                      let html = el.innerText;
+                      let children = [];
+                      let offset = 0;
+                      [...html.matchAll(/(?:[^\$]|^)(\$(?:\\.|[^\$])+\$)(?!\$)/g)].forEach((match) => {
+                                  let textBefore = html.substring(offset, match.index + 1);
+                                  children.push(document.createTextNode(textBefore));
+                                  let math = match[1].substring(1, match[1].length - 1);
+                                  let span = document.createElement("span");
+                                  katex.render(math, span, {displayMode: false, throwOnError: false});
+                                  children.push(span);
+                                  offset = match.index + match[0].length;
+                                });
+                      if (offset == 0) {
+                                  return;
+                                }
+                      let textAfter = html.substring(offset);
+                      if (textAfter.length > 0) {
+                                  children.push(document.createTextNode(textAfter));
+                                }
+                      while (el.firstChild) { el.firstChild.remove(); }
+                      children.forEach((child) => el.appendChild(child));
+                    });
       });
-      if (offset == 0) {
-        return;
-      }
-      let textAfter = html.substring(offset);
-      if (textAfter.length > 0) {
-        children.push(document.createTextNode(textAfter));
-      }
-      while (el.firstChild) { el.firstChild.remove(); }
-      children.forEach((child) => el.appendChild(child));
-    });
-  });
 </script>

src/basis_function/detail.rs

@@ -20,7 +20,7 @@ where
         if params.len() != Self::ARGUMENT_COUNT {
             panic!("Basisfunction expected {} arguments but the provided parameter slice has {} elements.",Self::ARGUMENT_COUNT,params.len());
         }
-        (&self)(x, params[0].clone())
+        (self)(x, params[0].clone())
     }
 
     const ARGUMENT_COUNT: usize = 1;

src/linalg_helpers/mod.rs

@@ -8,7 +8,7 @@ use std::ops::Mul;
 /// This internally stores only the diagonal elements
 /// # Types
 /// ScalarType: the numeric type of the matrix
-#[derive(Debug, Clone, PartialEq)]
+#[derive(Debug, Clone, PartialEq, Eq)]
 pub struct DiagDMatrix<ScalarType>
 where
     ScalarType: Scalar + ComplexField,

src/model/builder/error.rs

@@ -1,8 +1,8 @@
 use snafu::Snafu;
 
 /// An error structure that contains error variants that occur when building a model.
-#[derive(Debug, Clone, Snafu, PartialEq)]
-#[snafu(visibility = "pub")]
+#[derive(Debug, Clone, Snafu, PartialEq, Eq)]
+#[snafu(visibility(pub))]
 pub enum ModelBuildError {
     /// Model or function parameters contain duplicates
     #[snafu(display("Parameter list {:?} contains duplicates! Parameter lists must comprise only unique elements.",function_parameters))]

src/model/errors.rs

@@ -1,8 +1,8 @@
 use snafu::Snafu;
 
 /// Errors pertaining to use errors of the [SeparableModel].
-#[derive(Debug, Clone, Snafu, PartialEq)]
-#[snafu(visibility = "pub")]
+#[derive(Debug, Clone, Snafu, PartialEq, Eq)]
+#[snafu(visibility(pub))]
 pub enum ModelError {
     /// Base functions are expected to return a vector the same length as the location argument.
     /// A function did not adhere to that rule.

src/solvers/levmar/builder.rs

@@ -8,8 +8,8 @@ use snafu::Snafu;
 use std::ops::Mul;
 
 /// Errors pertaining to use errors of the [LeastSquaresProblemBuilder]
-#[derive(Debug, Clone, Snafu, PartialEq)]
-#[snafu(visibility = "pub")]
+#[derive(Debug, Clone, Snafu, PartialEq, Eq)]
+#[snafu(visibility(pub))]
 pub enum LevMarBuilderError {
     /// the data for the independent variable was not given to the builder
     #[snafu(display("Data for vector x not provided."))]

src/solvers/levmar/weights.rs

@@ -6,7 +6,7 @@ use std::ops::Mul;
 /// Right now covers only either unit weights (i.e. unweighted problem) or a diagonal
 /// matrix for the weights. Can easily be extended in the future, because this structure
 /// offers an interface for matrix-matrix multiplication and matrix-vector multiplication
-#[derive(Debug, Clone, PartialEq)]
+#[derive(Debug, Clone, PartialEq, Eq)]
 pub enum Weights<ScalarType>
 where
     ScalarType: Scalar + ComplexField,