Add proper documentation

3 files changed, 19 insertions, 575 deletions

diff --git a/.build.yml b/.build.yml
index d638df8..6e567e2 100644
--- a/.build.yml
+++ b/.build.yml
@@ -3,11 +3,19 @@ packages:
   - emacs-nox
   - hugo
   - zip
+  - rsync
 sources:
   - https://git.sr.ht/~ymherklotz/vericert-docs
 secrets:
   - fbcab77b-bd56-4356-a6b3-54c656f2b364
+  - f1c07b45-32bd-4559-b370-28e59e4c11e1
 tasks:
+  - init: |
+      cd vericert-docs/static
+      sshopts="ssh -o StrictHostKeyChecking=no"
+      rsync --rsh="$sshopts" zk@leika.ymhg.org:~/docs.tar.xz .
+      tar xvf docs.tar.xz
+      rm docs.tar.xz
   - build: |
       cd vericert-docs
       emacs --batch --file content.org --load publish.el
diff --git a/.gitignore b/.gitignore
index 68764a2..41a1ee7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,10 @@
 .DS_Store
 
 /content/
+/resources/
+
+/static/manual/
+/static/man/
+/static/src/
+
+*.lock
diff --git a/content.org b/content.org
index b702c3a..747f486 100644
--- a/content.org
+++ b/content.org
@@ -26,7 +26,8 @@ have all been proven correct, providing a verified translation from C to Verilog
 
 ** Content
 
-- [[#building][Vericert Documentation]]
+- [[/manual/index.html][Vericert Manual]]
+- [[/src/toc.html][Vericert Source]]
 
 ** Papers
 
@@ -50,580 +51,8 @@ For contributing patches to the [[https://sr.ht/~ymherklotz/vericert/][sourcehut
 :EXPORT_HUGO_CUSTOM_FRONT_MATTER: :headless true
 :END:
 
-- [[#docs][Docs]]
-  - [[#building][Building]]
+- [[./static/manual/index.html][Vericert Manual]]
 
-* Documentation
-
-** Docs
-:PROPERTIES:
-:EXPORT_FILE_NAME: _index
-:EXPORT_HUGO_SECTION: docs
-:CUSTOM_ID: docs
-:END:
-
-Vericert translates C code into a hardware description language called Verilog, which can then be
-synthesised into hardware, to be placed onto a field-programmable gate array (FPGA) or
-application-specific integrated circuit (ASIC).
-
-#+attr_html: :width 600
-#+caption: Current design of Vericert, where HTL is an intermediate language representing a finite state machine with data-path (FSMD) and Verilog is the target language.
-#+name: fig:design
-[[./static/images/toolflow.svg]]
-
-The design shown in Figure [[fig:design]] shows how Vericert leverages an existing verified C compiler
-called [[https://compcert.org/compcert-C.html][CompCert]] to perform this translation.
-
-** Building Vericert
-:PROPERTIES:
-:EXPORT_FILE_NAME: building
-:EXPORT_HUGO_SECTION: docs
-:CUSTOM_ID: building
-:END:
-
-To build Vericert, the provided Makefile can be used. External dependencies are needed to build the
-project, which can be pulled in automatically with [[https://nixos.org/nix/][nix]] using the provided ~default.nix~ and ~shell.nix~
-files.
-
-The project is written in Coq, a theorem prover, which is extracted to OCaml so that it can then be
-compiled and executed. The dependencies of this project are the following:
-
-- [[https://coq.inria.fr/][Coq]]: theorem prover that is used to also program the HLS tool.
-- [[https://ocaml.org/][OCaml]]: the OCaml compiler to compile the extracted files.
-- [[https://github.com/ocaml/dune][dune]]: build tool for ocaml projects to gather all the ocaml files and compile them in the right
-  order.
-- [[http://gallium.inria.fr/~fpottier/menhir/][menhir]]: parser generator for ocaml.
-- [[https://github.com/ocaml/ocamlfind][findlib]] to find installed OCaml libraries.
-- [[https://gcc.gnu.org/][GCC]]: compiler to help build CompCert.
-
-These dependencies can be installed manually, or automatically through Nix.
-
-*** Downloading CompCert
-
-CompCert is added as a submodule in the ~lib/CompCert~ directory. It is needed to run the build
-process below, as it is the one dependency that is not downloaded by nix, and has to be downloaded
-together with the repository. To clone CompCert together with this project, you can run:
-
-#+begin_src shell
-git clone --recursive https://github.com/ymherklotz/vericert
-#+end_src
-
-If the repository is already cloned, you can run the following command to make sure that CompCert is
-also downloaded:
-
-#+begin_src shell
-git submodule update --init
-#+end_src
-
-*** Setting up Nix
-
-Nix is a package manager that can create an isolated environment so that the builds are
-reproducible. Once nix is installed, it can be used in the following way.
-
-To open a shell which includes all the necessary dependencies, one can use:
-
-#+begin_src shell
-nix-shell
-#+end_src
-
-which will open a shell that has all the dependencies loaded.
-
-*** Makefile build
-
-If the dependencies were installed manually, or if one is in the ~nix-shell~, the project can be built
-by running:
-
-#+begin_src shell
-make -j8
-#+end_src
-
-and installed locally, or under the ~PREFIX~ location using:
-
-#+begin_src shell
-make install
-#+end_src
-
-Which will install the binary in ~./bin/vericert~ by default. However, this can be changed by changing
-the ~PREFIX~ environment variable, in which case the binary will be installed in ~$PREFIX/bin/vericert~.
-
-*** Testing
-
-To test out ~vericert~ you can try the following examples which are in the test folder using the
-following:
-
-#+begin_src shell
-./bin/vericert test/loop.c -o loop.v
-./bin/vericert test/conditional.c -o conditional.v
-./bin/vericert test/add.c -o add.v
-#+end_src
-
-Or by running the test suite using the following command:
-
-#+begin_src shell
-make test
-#+end_src
-** Using Vericert
-:PROPERTIES:
-:EXPORT_FILE_NAME: using-vericert
-:EXPORT_HUGO_SECTION: docs
-:CUSTOM_ID: using-vericert
-:END:
-
-Vericert can be used to translate a subset of C into Verilog.  As a simple example, consider the
-following C file (~main.c~):
-
-#+begin_src C
-void matrix_multiply(int first[2][2], int second[2][2], int multiply[2][2]) {
-    int sum = 0;
-    for (int c = 0; c < 2; c++) {
-        for (int d = 0; d < 2; d++) {
-            for (int k = 0; k < 2; k++) {
-                sum = sum + first[c][k]*second[k][d];
-            }
-            multiply[c][d] = sum;
-            sum = 0;
-        }
-    }
-}
-
-int main() {
-    int f[2][2] = {{1, 2}, {3, 4}};
-    int s[2][2] = {{5, 6}, {7, 8}};
-    int m[2][2] = {{0, 0}, {0, 0}};
-
-    matrix_multiply(f, s, m);
-    return m[1][1];
-}
-#+end_src
-
-It can be compiled using the following command, assuming that vericert is somewhere on the path.
-
-#+begin_src shell
-vericert main.c -o main.v
-#+end_src
-
-The Verilog file contains a top-level test-bench, which can be given to any Verilog simulator to
-simulate the hardware, which should give the same result as executing the C code.  Using [[http://iverilog.icarus.com/][Icarus
-Verilog]] as an example:
-
-#+begin_src shell
-iverilog -o main_v main.v
-#+end_src
-
-When executing, it should therefore print the following:
-
-#+begin_src shell
-$ ./main_v
-finished: 50
-#+end_src
-
-This gives the same result as executing the C in the following way:
-
-#+begin_src shell
-$ gcc -o main_c main.c
-$ ./main_c
-$ echo $?
-50
-#+end_src
-
-** Unreleased Features
-:PROPERTIES:
-:EXPORT_FILE_NAME: unreleased
-:EXPORT_HUGO_SECTION: docs
-:CUSTOM_ID: unreleased-features
-:END:
-
-The following are unreleased features in Vericert that are currently being worked on and have not
-been completely proven correct yet.  Currently this includes features such as:
-
-- [[#scheduling][scheduling]],
-- [[#operation-chaining][operation chaining]],
-- [[#if-conversion][if-conversion]], and
-- [[#functions][functions]].
-
-This page gives some preliminary information on how the features are implemented and how the proofs
-for the features are being done.  Once these features are properly implemented, they will be added
-to the proper documentation.
-
-*** Scheduling
-:PROPERTIES:
-:CUSTOM_ID: scheduling
-:END:
-
-Scheduling is an optimisation which is used to run various instructions in parallel that are
-independent to each other.
-
-*** Operation Chaining
-:PROPERTIES:
-:CUSTOM_ID: operation-chaining
-:END:
-
-Operation chaining is an optimisation that can be added on to scheduling and allows for the
-sequential execution of instructions in a clock cycle, while executing other instructions in
-parallel in the same clock cycle.
-
-*** If-conversion
-:PROPERTIES:
-:CUSTOM_ID: if-conversion
-:END:
-
-If-conversion is an optimisation which can turn code with simple control flow into a single block
-(called a hyper-block), using predicated instructions.
-
-*** Functions
-:PROPERTIES:
-:CUSTOM_ID: functions
-:END:
-
-Functions are currently only inlined in Vericert, however, we are working on a proper interface to
-integrate function calls into the hardware.
-
-** Coq Style Guide
-  :PROPERTIES:
-  :CUSTOM_ID: coq-style-guide
-  :EXPORT_FILE_NAME: coq-style-guide
-  :EXPORT_HUGO_SECTION: docs
-  :END:
-
-This style guide was taken from [[https://github.com/project-oak/silveroak][Silveroak]], it outlines code style for Coq code in this
-repository. There are certainly other valid strategies and opinions on Coq code style; this is laid
-out purely in the name of consistency. For a visual example of the style, see the [[#example][example]] at the
-bottom of this file.
-
-*** Code organization
-   :PROPERTIES:
-   :CUSTOM_ID: code-organization
-   :END:
-**** Legal banner
-    :PROPERTIES:
-    :CUSTOM_ID: legal-banner
-    :END:
-
-- Files should begin with a copyright/license banner, as shown in the example above.
-
-**** Import statements
-    :PROPERTIES:
-    :CUSTOM_ID: import-statements
-    :END:
-
-- =Require Import= statements should all go at the top of the file, followed by file-wide =Import=
-  statements.
-
-  - =Import=s often contain notations or typeclass instances that might override notations or
-    instances from another library, so it's nice to highlight them separately.
-
-- One =Require Import= statement per line; it's easier to scan that way.
-- =Require Import= statements should use "fully-qualified" names (e.g. =Require Import
-  Coq.ZArith.ZArith= instead of =Require Import ZArith=).
-
-  - Use the =Locate= command to find the fully-qualified name!
-
-- =Require Import='s should go in the following order:
-
-  1. Standard library dependencies (start with =Coq.=)
-  2. External dependencies (anything outside the current project)
-  3. Same-project dependencies
-
-- =Require Import='s with the same root library (the name before the first =.=) should be grouped
-  together. Within each root-library group, they should be in alphabetical order (so =Coq.Lists.List=
-  before =Coq.ZArith.ZArith=).
-
-**** Notations and scopes
-    :PROPERTIES:
-    :CUSTOM_ID: notations-and-scopes
-    :END:
-
-- Any file-wide =Local Open Scope='s should come immediately after the =Import=s (see example).
-
-  - Always use =Local Open Scope=; just =Open Scope= will sneakily open the scope for those who import
-    your file.
-
-- Put notations in their own separate modules or files, so that those who import your file can
-  choose whether or not they want the notations.
-
-  - Conflicting notations can cause a lot of headache, so it comes in very handy to leave this
-    flexibility!
-
-*** Formatting
-   :PROPERTIES:
-   :CUSTOM_ID: formatting
-   :END:
-**** Line length
-    :PROPERTIES:
-    :CUSTOM_ID: line-length
-    :END:
-
-- Maximum line length 80 characters.
-
-  - Many Coq IDE setups divide the screen in half vertically and use only half to display source
-    code, so more than 80 characters can be genuinely hard to read on a laptop.
-
-**** Whitespace and indentation
-    :PROPERTIES:
-    :CUSTOM_ID: whitespace-and-indentation
-    :END:
-
-- No trailing whitespace.
-
-- Spaces, not tabs.
-
-- Files should end with a newline.
-
-  - Many editors do this automatically on save.
-
-- Colons may be either "English-spaced", with no space before the colon and one space after (=x: nat=)
-  or "French-spaced", with one space before and after (=x : nat=).
-
-- Default indentation is 2 spaces.
-
-  - Keeping this small prevents complex proofs from being indented ridiculously far, and matches IDE
-    defaults.
-
-- Use 2-space indents if inserting a line break immediately after:
-
-  - =Proof.=
-  - =fun <...> =>=
-  - =forall <...>,=
-  - =exists <....>,=
-
-- The style for indenting arguments in function application depends on where you make a line
-  break. If you make the line break immediately after the function name, use a 2-space
-  indent. However, if you make it after one or more arguments, align the next line with the first
-  argument:
-
-  #+begin_src coq
-    (Z.pow
-       1 2)
-    (Z.pow 1 2 3
-           4 5 6)
-  #+end_src
-
-- =Inductive= cases should not be indented. Example:
-
-  #+begin_src coq
-    Inductive Foo : Type :=
-    | FooA : Foo
-    | FooB : Foo
-    .
-  #+end_src
-
-- =match= or =lazymatch= cases should line up with the "m" in =match= or "l" in =lazymatch=, as in the
-  following examples:
-
-  #+begin_src coq
-    match x with
-    | 3 => true
-    | _ => false
-    end.
-
-    lazymatch x with
-    | 3 => idtac
-    | _ => fail "Not equal to 3:" x
-    end.
-
-    repeat match goal with
-           | _ => progress subst
-           | _ => reflexivity
-           end.
-
-    do 2 lazymatch goal with
-         | |- context [eq] => idtac
-         end.
-  #+end_src
-
-*** Definitions and Fixpoints
-   :PROPERTIES:
-   :CUSTOM_ID: definitions-and-fixpoints
-   :END:
-
-- It's okay to leave the return type of =Definition='s and =Fixpoint='s implicit (e.g. ~Definition x := 5~
-  instead of ~Definition x : nat := 5~) when the type is very simple or obvious (for instance, the
-  definition is in a file which deals exclusively with operations on =Z=).
-
-*** Inductives
-   :PROPERTIES:
-   :CUSTOM_ID: inductives
-   :END:
-
-- The =.= ending an =Inductive= can be either on the same line as the last case or on its own line
-  immediately below. That is, both of the following are acceptable:
-
-  #+begin_src coq
-    Inductive Foo : Type :=
-    | FooA : Foo
-    | FooB : Foo
-    .
-    Inductive Foo : Type :=
-    | FooA : Foo
-    | FooB : Foo.
-  #+end_src
-
-*** Lemma/Theorem statements
-   :PROPERTIES:
-   :CUSTOM_ID: lemmatheorem-statements
-   :END:
-
-- Generally, use =Theorem= for the most important, top-level facts you prove and =Lemma= for everything
-  else.
-- Insert a line break after the colon in the lemma statement.
-- Insert a line break after the comma for =forall= or =exist= quantifiers.
-- Implication arrows (=->=) should share a line with the previous hypothesis, not the following one.
-- There is no need to make a line break after every =->=; short preconditions may share a line.
-
-*** Proofs and tactics
-   :PROPERTIES:
-   :CUSTOM_ID: proofs-and-tactics
-   :END:
-
-- Use the =Proof= command (lined up vertically with =Lemma= or =Theorem= it corresponds to) to open a
-  proof, and indent the first line after it 2 spaces.
-
-- Very small proofs (where =Proof. <tactics> Qed.= is <= 80 characters) can go all in one line.
-
-- When ending a proof, align the ending statement (=Qed=, =Admitted=, etc.) with =Proof=.
-
-- Avoid referring to autogenerated names (e.g. =H0=, =n0=). It's okay to let Coq generate these names,
-  but you should not explicitly refer to them in your proof. So =intros; my_solver= is fine, but
-  =intros; apply H1; my_solver= is not fine.
-
-  - You can force a non-autogenerated name by either putting the variable before the colon in the
-    lemma statement (=Lemma foo x : ...= instead of =Lemma foo : forall x, ...=), or by passing
-    arguments to =intros= (e.g. =intros ? x= to name the second argument =x=)
-
-- This way, the proof won't break when new hypotheses are added or autogenerated variable names
-  change.
-
-- Use curly braces ={}= for subgoals, instead of bullets.
-
-- /Never write tactics with more than one subgoal focused./ This can make the proof very confusing to
-  step through! If you have more than one subgoal, use curly braces.
-
-- Consider adding a comment after the opening curly brace that explains what case you're in (see
-  example).
-
-  - This is not necessary for small subgoals but can help show the major lines of reasoning in large
-    proofs.
-
-- If invoking a tactic that is expected to return multiple subgoals, use =[ | ... | ]= before the =.= to
-  explicitly specify how many subgoals you expect.
-
-  - Examples: =split; [ | ].= =induction z; [ | | ].=
-  - This helps make code more maintainable, because it fails immediately if your tactic no longer
-    solves as many subgoals as expected (or unexpectedly solves more).
-
-- If invoking a string of tactics (composed by =;=) that will break the goal into multiple subgoals
-  and then solve all but one, still use =[ ]= to enforce that all but one goal is solved.
-
-  - Example: =split; try lia; [ ]=.
-
-- Tactics that consist only of =repeat=-ing a procedure (e.g. =repeat match=, =repeat first=) should
-  factor out a single step of that procedure a separate tactic called =<tactic name>_step=, because
-  the single-step version is much easier to debug. For instance:
-
-  #+begin_src coq
-    Ltac crush_step :=
-      match goal with
-      | _ => progress subst
-      | _ => reflexivity
-      end.
-    Ltac crush := repeat crush_step.
-  #+end_src
-
-*** Naming
-   :PROPERTIES:
-   :CUSTOM_ID: naming
-   :END:
-
-- Helper proofs about standard library datatypes should go in a module that is named to match the
-  standard library module (see example).
-
-  - This makes the helper proofs look like standard-library ones, which is helpful for categorizing
-    them if they're genuinely at the standard-library level of abstraction.
-
-- Names of modules should start with capital letters.
-- Names of inductives and their constructors should start with capital letters.
-- Names of other definitions/lemmas should be snake case.
-
-*** Example
-   :PROPERTIES:
-   :CUSTOM_ID: example
-   :END:
-A small standalone Coq file that exhibits many of the style points.
-
-#+begin_src coq
-(*
- * Vericert: Verified high-level synthesis.
- * Copyright (C) 2021 Name <email@example.com>
- *
- * <License...>
- *)
-
-  Require Import Coq.Lists.List.
-  Require Import Coq.micromega.Lia.
-  Require Import Coq.ZArith.ZArith.
-  Import ListNotations.
-  Local Open Scope Z_scope.
-
-  (* Helper proofs about standard library integers (Z) go within [Module Z] so
-     that they match standard-library Z lemmas when used. *)
-  Module Z.
-    Lemma pow_3_r x : x ^ 3 = x * x * x.
-    Proof. lia. Qed. (* very short proofs can go all on one line *)
-
-    Lemma pow_4_r x : x ^ 4 = x * x * x * x.
-    Proof.
-      change 4 with (Z.succ (Z.succ (Z.succ (Z.succ 0)))).
-      repeat match goal with
-             | _ => rewrite Z.pow_1_r
-             | _ => rewrite Z.pow_succ_r by lia
-             | |- context [x * (?a * ?b)] =>
-               replace (x * (a * b)) with (a * b * x) by lia
-             | _ => reflexivity
-             end.
-    Qed.
-  End Z.
-  (* Now we can access the lemmas above as Z.pow_3_r and Z.pow_4_r, as if they
-     were in the ZArith library! *)
-
-  Definition bar (x y : Z) := x ^ (y + 1).
-
-  (* example with a painfully manual proof to show case formatting *)
-  Lemma bar_upper_bound :
-    forall x y a,
-      0 <= x <= a -> 0 <= y ->
-      0 <= bar x y <= a ^ (y + 1).
-  Proof.
-    (* avoid referencing autogenerated names by explicitly naming variables *)
-    intros x y a Hx Hy. revert y Hy x a Hx.
-    (* explicitly indicate # subgoals with [ | ... | ] if > 1 *)
-    cbv [bar]; refine (natlike_ind _ _ _); [ | ].
-    { (* y = 0 *)
-      intros; lia. }
-    { (* y = Z.succ _ *)
-      intros.
-      rewrite Z.add_succ_l, Z.pow_succ_r by lia.
-      split.
-      { (* 0 <= bar x y *)
-        apply Z.mul_nonneg_nonneg; [ lia | ].
-        apply Z.pow_nonneg; lia. }
-      { (* bar x y < a ^ y *)
-        rewrite Z.pow_succ_r by lia.
-        apply Z.mul_le_mono_nonneg; try lia;
-          [ apply Z.pow_nonneg; lia | ].
-        (* For more flexible proofs, use match statements to find hypotheses
-           rather than referring to them by autogenerated names like H0. In this
-           case, we'll take any hypothesis that applies to and then solves the
-           goal. *)
-        match goal with H : _ |- _ => apply H; solve [auto] end. } }
-  Qed.
-
-  (* Put notations in a separate module or file so that importers can
-     decide whether or not to use them. *)
-  Module BarNotations.
-    Infix "#" := bar (at level 40) : Z_scope.
-    Notation "x '##'" := (bar x x) (at level 40) : Z_scope.
-  End BarNotations.
-#+end_src
 * Blog
 ** Blog
 :PROPERTIES:
@@ -849,7 +278,7 @@ parallel.
 Loop pipelining is an optimisation to schedule loops, instead of only scheduling the instructions
 inside of the loop.  There are two versions of loop pipelining, software and hardware loop
 pipelining.  The former is done purely on instructions, whereas the latter is performed in tandem
-with [[#scheduling][scheduling]].
+with [[/manual/Scheduling.html][scheduling]].
 
 * Footnotes
 [fn:2] One example is with the ~Oshrximm~ instruction, which is represented using division in