From af5b92e5a82a99e1e54e88aaafef1649c8b4c210 Mon Sep 17 00:00:00 2001
From: Reno <25192197+singularitti@users.noreply.github.com>
Date: Mon, 5 Jul 2021 03:19:53 -0400
Subject: [PATCH 01/13] Remove Spglib.jl from deps

---
 Project.toml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/Project.toml b/Project.toml
index 38e380b..2ba4472 100644
--- a/Project.toml
+++ b/Project.toml
@@ -7,13 +7,11 @@ version = "0.1.1"
 CoordinateTransformations = "150eb455-5306-5404-9cee-2592286d6298"
 CrystallographyBase = "93b1d1cd-a8ea-4aa5-adb1-b2407ea0ba8d"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-Spglib = "f761d5c5-86db-4880-b97f-9680a7cccfb5"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 
 [compat]
 CoordinateTransformations = "0.5, 0.6"
 CrystallographyBase = "0.1"
-Spglib = "0.1, 0.2"
 StaticArrays = "0.8.3, 0.9, 0.10, 0.11, 0.12, 1"
 julia = "1"
 

From 79ebf58ff95ec9f300e945924cba7cf522ec9b25 Mon Sep 17 00:00:00 2001
From: Reno <25192197+singularitti@users.noreply.github.com>
Date: Mon, 5 Jul 2021 03:23:45 -0400
Subject: [PATCH 02/13] Fix imports from CrystallographyBase.jl

---
 src/Crystallography.jl | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/Crystallography.jl b/src/Crystallography.jl
index a3acae8..7153f7b 100644
--- a/src/Crystallography.jl
+++ b/src/Crystallography.jl
@@ -41,8 +41,8 @@ using CrystallographyBase:
     ReciprocalLattice,
     Miller,
     MillerBravais,
-    RealSpace,
-    ReciprocalSpace,
+    ReciprocalMiller,
+    ReciprocalMillerBravais,
     FractionalFromCartesian,
     CartesianFromFractional,
     FractionalToCartesian,
@@ -62,9 +62,9 @@ using CrystallographyBase:
     reciprocal_mesh,
     coordinates,
     weights,
+    family,
     cellvolume,
-    @m_str,
-    @mb_str
+    @m_str
 
 export CrystalSystem,
     Triclinic,
@@ -107,8 +107,8 @@ export CrystalSystem,
     ReciprocalLattice,
     Miller,
     MillerBravais,
-    RealSpace,
-    ReciprocalSpace,
+    ReciprocalMiller,
+    ReciprocalMillerBravais,
     FractionalFromCartesian,
     CartesianFromFractional,
     FractionalToCartesian,
@@ -128,9 +128,9 @@ export centering,
     reciprocal_mesh,
     coordinates,
     weights,
+    family,
     cellvolume,
-    @m_str,
-    @mb_str
+    @m_str
 
 include("Symmetry.jl")
 

From 9e153ea448b723fdca7ab2bac7cece6ed1ccbb1e Mon Sep 17 00:00:00 2001
From: Reno <25192197+singularitti@users.noreply.github.com>
Date: Mon, 5 Jul 2021 03:24:57 -0400
Subject: [PATCH 03/13] Comment Symmetry.jl

---
 src/Crystallography.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Crystallography.jl b/src/Crystallography.jl
index 7153f7b..e7de4b4 100644
--- a/src/Crystallography.jl
+++ b/src/Crystallography.jl
@@ -132,6 +132,6 @@ export centering,
     cellvolume,
     @m_str
 
-include("Symmetry.jl")
+# include("Symmetry.jl")
 
 end

From 1ef5d6c4da0952249a0b6bab72b9beea7d4a350c Mon Sep 17 00:00:00 2001
From: Reno <25192197+singularitti@users.noreply.github.com>
Date: Mon, 5 Jul 2021 03:32:14 -0400
Subject: [PATCH 04/13] Fix UUID in docs/Project.toml

---
 docs/Project.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/Project.toml b/docs/Project.toml
index ea07c29..4155109 100644
--- a/docs/Project.toml
+++ b/docs/Project.toml
@@ -1,3 +1,3 @@
 [deps]
-Crystallography = "06308cd2-f292-494b-9308-80930bf85278"
+Crystallography = "3bff3928-7a76-11e9-2089-d112443085a5"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"

From 279636247106f666b9d0a55ae6e6a74e23af7412 Mon Sep 17 00:00:00 2001
From: Reno <25192197+singularitti@users.noreply.github.com>
Date: Mon, 5 Jul 2021 03:33:02 -0400
Subject: [PATCH 05/13] Fix make.jl

---
 docs/make.jl | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/docs/make.jl b/docs/make.jl
index cfc39b7..a7d496e 100644
--- a/docs/make.jl
+++ b/docs/make.jl
@@ -15,10 +15,9 @@ makedocs(;
     ),
     pages=[
         "Home" => "index.md",
-        "Manual" => Any["Installation"=>"install.md", "Development"=>"develop.md"],
+        "Manual" => Any["Installation"=>"installation.md", "Development"=>"develop.md"],
         "API by modules" => Any[
-            "`Crystallography` module"=>"Crystallography.md",
-            "`Crystallography.Symmetry` module"=>"Symmetry.md",
+            "`Crystallography` module"=>"api.md",
         ],
     ],
 )

From b27599de942463334727dbf3254b942cb9b7b279 Mon Sep 17 00:00:00 2001
From: Reno <25192197+singularitti@users.noreply.github.com>
Date: Mon, 5 Jul 2021 03:33:15 -0400
Subject: [PATCH 06/13] Update docs/src/installation.md

---
 docs/src/{install.md => installation.md} | 27 ++++++++++++++++++++++--
 1 file changed, 25 insertions(+), 2 deletions(-)
 rename docs/src/{install.md => installation.md} (63%)

diff --git a/docs/src/install.md b/docs/src/installation.md
similarity index 63%
rename from docs/src/install.md
rename to docs/src/installation.md
index 295e620..46cbb6b 100644
--- a/docs/src/install.md
+++ b/docs/src/installation.md
@@ -1,9 +1,18 @@
 # Installation
 
+```@contents
+Pages = ["installation.md"]
+Depth = 3
+```
+
 To install this package, first, you need to install a `julia` executable from
-[its official website](https://julialang.org/downloads/). Version `v1.0.0` and
+[its official website](https://julialang.org/downloads/). Version `v1.3.0` and
 above is required. This package may not work on `v0.7` and below.
 
+## Installing Julia
+
+### on macOS
+
 If you are using a Mac, and have [Homebrew](https://brew.sh) installed, open
 `Terminal.app` and type:
 
@@ -11,6 +20,20 @@ If you are using a Mac, and have [Homebrew](https://brew.sh) installed, open
 brew cask install julia
 ```
 
+### on Linux
+
+On Linux, the best way to install Julia is to use the Generic Linux Binaries. The
+[JILL](https://github.com/abelsiqueira/jill) script does this for you. Just run
+
+```shell
+bash -ci "$(curl -fsSL https://raw.githubusercontent.com/abelsiqueira/jill/master/jill.sh)"
+```
+
+installs Julia into `$HOME/.local/bin`. This script also has a Python version,
+[JILL.py](https://github.com/johnnychen94/jill.py). It can also be used on macOS.
+
+## Installing the package
+
 Now I am using [macOS](https://en.wikipedia.org/wiki/MacOS) as a standard
 platform to explain the following steps:
 
@@ -21,7 +44,7 @@ platform to explain the following steps:
    ```julia
    julia> using Pkg; Pkg.update()
 
-   julia> Pkg.add(PackageSpec(url="https://github.com/MineralsCloud/Crystallography.jl.git"))
+   julia> Pkg.add("Crystallography")
    ```
 
    and wait for its finish.

From 5b787cdbc32e6d4eee428dab7f6cf3d62673beb9 Mon Sep 17 00:00:00 2001
From: Reno <25192197+singularitti@users.noreply.github.com>
Date: Mon, 5 Jul 2021 03:33:38 -0400
Subject: [PATCH 07/13] Rename docs/src/Crystallography.md to api.md

---
 docs/src/Crystallography.md |  8 ----
 docs/src/api.md             | 86 +++++++++++++++++++++++++++++++++++++
 2 files changed, 86 insertions(+), 8 deletions(-)
 delete mode 100644 docs/src/Crystallography.md
 create mode 100644 docs/src/api.md

diff --git a/docs/src/Crystallography.md b/docs/src/Crystallography.md
deleted file mode 100644
index 2bc797f..0000000
--- a/docs/src/Crystallography.md
+++ /dev/null
@@ -1,8 +0,0 @@
-```@contents
-Pages = ["Crystals.md"]
-Depth = 3
-```
-
-```@autodocs
-Modules = [Crystallography]
-```
diff --git a/docs/src/api.md b/docs/src/api.md
new file mode 100644
index 0000000..eec6f8e
--- /dev/null
+++ b/docs/src/api.md
@@ -0,0 +1,86 @@
+```@meta
+CurrentModule = Crystallography
+```
+
+# API
+
+```@contents
+Pages = ["api.md"]
+Depth = 3
+```
+
+### Lattice
+
+```@docs
+CrystalSystem
+Triclinic
+Monoclinic
+Orthorhombic
+Tetragonal
+Cubic
+Trigonal
+Hexagonal
+Centering
+BaseCentering
+Primitive
+BodyCentering
+FaceCentering
+RhombohedralCentering
+BaseCentering
+Bravais
+Lattice
+centering
+crystalsystem
+basis_vectors
+cellparameters
+supercell
+```
+
+### Reciprocal space
+
+Note that we take ``2pi`` as ``1``, not the solid-state physics convention.
+
+```@docs
+ReciprocalPoint
+ReciprocalLattice
+inv
+reciprocal_mesh
+coordinates
+weights
+```
+
+### Miller and Miller–Bravais indices
+
+```@docs
+Miller
+MillerBravais
+ReciprocalMiller
+ReciprocalMillerBravais
+family
+@m_str
+```
+
+### Metric tensor
+
+```@docs
+MetricTensor
+directioncosine
+directionangle
+distance
+interplanar_spacing
+```
+
+### Transformations
+
+```@docs
+CartesianFromFractional
+FractionalFromCartesian
+PrimitiveFromStandardized
+StandardizedFromPrimitive
+```
+
+### Others
+
+```@docs
+cellvolume
+```

From b799f31da93ab691c035e6ce5604e6d0ed062ab7 Mon Sep 17 00:00:00 2001
From: Reno <25192197+singularitti@users.noreply.github.com>
Date: Mon, 5 Jul 2021 03:33:45 -0400
Subject: [PATCH 08/13] Remove docs/src/Symmetry.md

---
 docs/src/Symmetry.md | 8 --------
 1 file changed, 8 deletions(-)
 delete mode 100644 docs/src/Symmetry.md

diff --git a/docs/src/Symmetry.md b/docs/src/Symmetry.md
deleted file mode 100644
index 0bd516d..0000000
--- a/docs/src/Symmetry.md
+++ /dev/null
@@ -1,8 +0,0 @@
-```@contents
-Pages = ["Symmetry.md"]
-Depth = 3
-```
-
-```@autodocs
-Modules = [Crystallography.Symmetry]
-```

From 9baae130824ef802e4a09021819e8b7a892d88d4 Mon Sep 17 00:00:00 2001
From: Reno <25192197+singularitti@users.noreply.github.com>
Date: Mon, 5 Jul 2021 03:34:00 -0400
Subject: [PATCH 09/13] Fix docs/src/develop.md

---
 docs/src/develop.md | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/docs/src/develop.md b/docs/src/develop.md
index 27f5d66..75f1b01 100644
--- a/docs/src/develop.md
+++ b/docs/src/develop.md
@@ -1,23 +1,20 @@
-# How to develop this package by yourself
+# How to contribute
 
 ## Download the project
 
-Similar to what we have mentioned in section "[Installation](@ref)", instead of running
+Similar to section "[Installation](@ref)", run
 
 ```julia
-julia> Pkg.add(PackageSpec(url="https://github.com/MineralsCloud/Crystallography.jl.git"))
-```
-
-run
+julia> using Pkg
 
-```julia
-julia> Pkg.dev(PackageSpec(url="https://github.com/MineralsCloud/Crystallography.jl.git"))
+julia> pkg"dev Crystallography"
 ```
 
+in Julia REPL.
+
 Then the package will be cloned to your local machine at a path. On macOS, by default is
 located at `~/.julia/dev/Crystallography` unless you modify the `JULIA_DEPOT_PATH`
-environment variable. (See [Julia's official
-documentation](http://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_DEPOT_PATH-1)
+environment variable. (See [Julia's official documentation](http://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_DEPOT_PATH-1)
 on how to do this.) In the following text, we will call it `PKGROOT`.
 
 ## [Instantiate the project](@id instantiating)
@@ -30,6 +27,10 @@ julia> using Pkg; Pkg.instantiate()
 
 ## How to build docs
 
+Usually, the up-to-state doc is available in
+[here](https://mineralscloud.github.io/Crystallography.jl/dev/), but there are cases
+where users need to build the doc themselves.
+
 After [instantiating](@ref) the project, go to `PKGROOT`, run (without the `$` prompt)
 
 ```bash

From ee7cc974a7e17381ffd0b9f77dcab3f356e26b41 Mon Sep 17 00:00:00 2001
From: Reno <25192197+singularitti@users.noreply.github.com>
Date: Mon, 5 Jul 2021 03:34:13 -0400
Subject: [PATCH 10/13] Fix docs/src/index.md

---
 docs/src/index.md | 38 +++++++++++++++++++++++++++++++++++---
 1 file changed, 35 insertions(+), 3 deletions(-)

diff --git a/docs/src/index.md b/docs/src/index.md
index 9eb17ce..c295e02 100644
--- a/docs/src/index.md
+++ b/docs/src/index.md
@@ -6,9 +6,41 @@ CurrentModule = Crystallography
 
 Documentation for [Crystallography](https://github.com/MineralsCloud/Crystallography.jl).
 
-```@index
+## Package Features
+
+Provides some types and methods for crystallography calculations.
+
+See the [Index](@ref main-index) for the complete list of documented functions
+and types.
+
+The code is [hosted on GitHub](https://github.com/MineralsCloud/Crystallography.jl),
+with some continuous integration services to test its validity.
+
+This repository is created and maintained by [singularitti](https://github.com/singularitti).
+You are very welcome to contribute.
+
+## Compatibility
+
+- [Julia version: `v1.3.0` to `v1.6.1`](https://julialang.org/downloads/)
+- Dependencies:
+  - [`CoordinateTransformations.jl`](https://github.com/JuliaGeometry/CoordinateTransformations.jl) `v0.5.1` and above
+  - [`CrystallographyBase.jl`](https://github.com/MineralsCloud/CrystallographyBase.jl) `v0.1.0` and above
+  - [`StaticArrays.jl`](https://github.com/JuliaArrays/StaticArrays.jl) `v0.8.3` and above
+- OS: macOS, Linux, Windows, and FreeBSD
+- Architecture: x86, x64, ARM
+
+## Manual Outline
+
+```@contents
+Pages = [
+    "installation.md",
+    "develop.md",
+    "api.md",
+]
+Depth = 3
 ```
 
-```@autodocs
-Modules = [Crystallography]
+## [Index](@id main-index)
+
+```@index
 ```

From 95a1f898be4474ab32da56b94715684c3b4e1ccf Mon Sep 17 00:00:00 2001
From: Reno <25192197+singularitti@users.noreply.github.com>
Date: Mon, 5 Jul 2021 03:36:45 -0400
Subject: [PATCH 11/13] Add CONTRIBUTING.md

---
 CONTRIBUTING.md | 1 +
 1 file changed, 1 insertion(+)
 create mode 120000 CONTRIBUTING.md

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
new file mode 120000
index 0000000..e3019c3
--- /dev/null
+++ b/CONTRIBUTING.md
@@ -0,0 +1 @@
+docs/src/develop.md
\ No newline at end of file

From b183c98f9013fc6b4df9ad518dab31a5f11a0560 Mon Sep 17 00:00:00 2001
From: Reno <25192197+singularitti@users.noreply.github.com>
Date: Mon, 5 Jul 2021 03:38:01 -0400
Subject: [PATCH 12/13] Remove CONTRIBUTING.md

---
 CONTRIBUTING.md | 1 -
 1 file changed, 1 deletion(-)
 delete mode 120000 CONTRIBUTING.md

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
deleted file mode 120000
index e3019c3..0000000
--- a/CONTRIBUTING.md
+++ /dev/null
@@ -1 +0,0 @@
-docs/src/develop.md
\ No newline at end of file

From 5ec302d224900e2b38e79fcfb2e7f2b1710be445 Mon Sep 17 00:00:00 2001
From: Reno <25192197+singularitti@users.noreply.github.com>
Date: Mon, 5 Jul 2021 03:48:02 -0400
Subject: [PATCH 13/13] Fix CrystallographyBase.jl functions won't build

---
 docs/Project.toml | 1 +
 docs/make.jl      | 3 ++-
 docs/src/api.md   | 2 +-
 3 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/docs/Project.toml b/docs/Project.toml
index 4155109..96d9f6a 100644
--- a/docs/Project.toml
+++ b/docs/Project.toml
@@ -1,3 +1,4 @@
 [deps]
 Crystallography = "3bff3928-7a76-11e9-2089-d112443085a5"
+CrystallographyBase = "93b1d1cd-a8ea-4aa5-adb1-b2407ea0ba8d"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
diff --git a/docs/make.jl b/docs/make.jl
index a7d496e..4923fc2 100644
--- a/docs/make.jl
+++ b/docs/make.jl
@@ -1,10 +1,11 @@
 using Crystallography
+using CrystallographyBase
 using Documenter
 
 DocMeta.setdocmeta!(Crystallography, :DocTestSetup, :(using Crystallography); recursive=true)
 
 makedocs(;
-    modules=[Crystallography],
+    modules=[Crystallography,CrystallographyBase],
     authors="Qi Zhang <singularitti@outlook.com>",
     repo="https://github.com/MineralsCloud/Crystallography.jl/blob/{commit}{path}#{line}",
     sitename="Crystallography.jl",
diff --git a/docs/src/api.md b/docs/src/api.md
index eec6f8e..4e8131b 100644
--- a/docs/src/api.md
+++ b/docs/src/api.md
@@ -1,5 +1,5 @@
 ```@meta
-CurrentModule = Crystallography
+CurrentModule = CrystallographyBase
 ```
 
 # API