Tracking Changes

Interact

Adding files and the staging area

First let’s make sure we’re still in the right directory. You should be in the planets directory.

pwd

/home/stuart/Git/Aperio/stfc_website/notebooks/02-git

If you are still in moons, navigate back up to planets

pwd

/home/stuart/Git/Aperio/stfc_website/notebooks/02-git



cd ..

Let’s create a file called mars.txt that contains some notes about the Red Planet’s suitability as a base. We’ll use nano to edit the file; you can use whatever editor you like. In particular, this does not have to be the core.editor you set globally earlier. But remember, the bash command to create or edit a new file will depend on the editor you choose (it might not be nano). For a refresher on text editors, check out “Which Editor?” in The Unix Shell lesson.

$ nano mars.txt

Type the text below into the mars.txt file:

Cold and dry, but everything is my favorite color

mars.txt now contains a single line, which we can see by running:

ls

00-lessons.ipynb             02-git                     05-writing-effective-tests  08-sunpy-and-astropy  11-tabular-data              14-searching-and-downloading-data  README
00-lessons_instructor.ipynb  03-fundamentals-of-python  06-approximating-pi         09-time-series-data   12-images-and-visualisation  15-final-exercise                  environment.yml
01-bash                      04-further-python          07-collaborating-with-git   10-units              13-images-in-astronomy       LICENCE



cat mars.txt

If we check the status of our project again, Git tells us that it’s noticed the new file:

git status

On branch master
Your branch is up to date with 'origin/master'.

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

	modified:   02-git/02-creating-repositories_instructor.ipynb

no changes added to commit (use "git add" and/or "git commit -a")

The “untracked files” message means that there’s a file in the directory that Git isn’t keeping track of. We can tell Git to track a file using git add:

git add mars.txt

and then check that the right thing happened:

git status

On branch master
Your branch is up to date with 'origin/master'.

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

	modified:   02-git/02-creating-repositories_instructor.ipynb

no changes added to commit (use "git add" and/or "git commit -a")

Git now knows that it’s supposed to keep track of mars.txt, but it hasn’t recorded these changes as a commit yet. To get it to do that, we need to run one more command:

git commit -m "Start notes on Mars as a base"

On branch master
Your branch is up to date with 'origin/master'.

Changes not staged for commit:
	modified:   02-git/02-creating-repositories_instructor.ipynb

no changes added to commit

When we run git commit, Git takes everything we have told it to save by using git add and stores a copy permanently inside the special .git directory. This permanent copy is called a commit (or revision) and its short identifier is f22b25e. Your commit may have another identifier.

We use the -m flag (for “message”) to record a short, descriptive, and specific comment that will help us remember later on what we did and why. If we just run git commit without the -m option, Git will launch nano (or whatever other editor we configured as core.editor) so that we can write a longer message.

Good commit messages start with a brief (<50 characters) statement about the changes made in the commit. Generally, the message should complete the sentence “If applied, this commit will” . If you want to go into more detail, add a blank line between the summary line and your additional notes. Use this additional space to explain why you made changes and/or what their impact will be.

If we run git status now:

git status

On branch master
Your branch is up to date with 'origin/master'.

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

	modified:   02-git/02-creating-repositories_instructor.ipynb

no changes added to commit (use "git add" and/or "git commit -a")

it tells us everything is up to date. If we want to know what we’ve done recently, we can ask Git to show us the project’s history using git log:

git log

commit f922c9fa07facba0faa14d2174fcf5c27852eb2a (HEAD -> master, origin/master, origin/HEAD)
Author: Stuart Mumford <stuart@cadair.com>
Date:   Thu Sep 6 18:15:11 2018 +0100

    update notebooks

commit 6053bb89d157b173dda754a895ca3f1076cde97d
Author: Stuart Mumford <stuart@cadair.com>
Date:   Thu Sep 6 12:23:57 2018 +0100

    update notebooks

commit 51172805ab324552bca7a9427eb966a743b4fada
Author: Stuart Mumford <stuart@cadair.com>
Date:   Thu Sep 6 12:03:57 2018 +0100

    update notebooks

commit d26b47bc47fa5768ea2073e3b9683c49a6889908
Author: Stuart Mumford <stuart@cadair.com>
Date:   Thu Sep 6 11:28:09 2018 +0100

    update notebooks

commit 6637293dcb50ae76c9e4a0bf1e2b08dd5a6ce913
Author: Stuart Mumford <stuart@cadair.com>
Date:   Thu Sep 6 11:05:50 2018 +0100

    update notebooks

commit 35247321b5a0ac13471f18bb4703270d94432b73
Author: Stuart Mumford <stuart@cadair.com>
Date:   Wed Sep 5 23:03:45 2018 +0100

    update notebooks

commit 58f1a7f5ee4193bcbf72b15979a8f01a1b99a450
Author: Stuart Mumford <stuart@cadair.com>
Date:   Wed Sep 5 22:28:02 2018 +0100

    update notebooks

commit a967806ebde74eae9d044a895c1651e22e8e0819
Author: Stuart Mumford <stuart@cadair.com>
Date:   Wed Sep 5 16:29:44 2018 +0100

    update notebooks

commit d47a0802cc1913b5073992f9b6fbcc0b72c86307
Author: Stuart Mumford <stuart@cadair.com>
Date:   Wed Sep 5 13:52:51 2018 +0100

    add the csv for timeseries

commit 4135ff84e2b4a552317e7087ae14fdbf0093a2eb
Author: Stuart Mumford <stuart@cadair.com>
Date:   Wed Sep 5 13:51:07 2018 +0100

    update notebooks

commit a9991e8dada1d4de009f1f650a8da84bcfd8757f
Author: Stuart Mumford <stuart@cadair.com>
Date:   Tue Sep 4 11:25:33 2018 +0100

    update notebooks

commit 5bb6f9a228823fb5890d2c0d6b2e9c0b03673668
Author: Stuart Mumford <stuart@cadair.com>
Date:   Tue Sep 4 08:41:44 2018 +0100

    update notebooks

commit dd2848367dff52dd13db252e688a085b0638d2c7
Author: Stuart Mumford <stuart@cadair.com>
Date:   Mon Sep 3 13:24:05 2018 +0100

    update notebooks

commit d3568a1b07b9bf76d89803e610c8ece8d4b94a81
Author: Stuart Mumford <stuart@cadair.com>
Date:   Sun Sep 2 19:25:16 2018 +0100

    update notebooks

commit f5844e2671a8c7a2b212214a4f6c8bd72428f7c3
Author: Stuart Mumford <stuart@cadair.com>
Date:   Sun Sep 2 14:51:57 2018 +0100

    rename to avoid website issues

commit ffe8c9dd48510cd2dcbb964c8ead21b93912be21
Author: Stuart Mumford <stuart@cadair.com>
Date:   Sun Sep 2 14:43:57 2018 +0100

    update notebooks

commit 801632edee8fc310d8500bfaeea8651f099283b3
Author: Stuart Mumford <stuart@cadair.com>
Date:   Sun Sep 2 14:43:13 2018 +0100

    update notebooks

commit 9c74198bf838b7f7127d8fab527e4d96aab72e08
Author: Stuart Mumford <stuart@cadair.com>
Date:   Sun Sep 2 13:46:49 2018 +0100

    Add licence and readme to the lessons repo

commit 08b3d7073b526396de7e31ec6e8bd65d075207b6
Author: Stuart Mumford <stuart@cadair.com>
Date:   Sun Sep 2 12:59:07 2018 +0100

    Add initial dump of rendered lessons

git log lists all commits made to a repository in reverse chronological order. The listing for each commit includes the commit’s full identifier (which starts with the same characters as the short identifier printed by the git commit command earlier), the commit’s author, when it was created, and the log message Git was given when the commit was created.

# Where Are My Changes?

If we run ls at this point, we will still see just one file called mars.txt. That’s because Git saves information about files’ history in the special .git directory mentioned earlier so that our filesystem doesn’t become cluttered (and so that we can’t accidentally edit or delete an old version).

Now suppose Dracula adds more information to the file. (Again, we’ll edit with nano and then cat the file to show its contents; you may use a different editor, and don’t need to cat.)

nano mars.txt
cat mars.txt





Cold and dry, but everything is my favorite color
The two moons may be a problem for Wolfman

When we run git status now, it tells us that a file it already knows about has been modified:

git status

On branch master
Your branch is up to date with 'origin/master'.

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

	modified:   02-git/02-creating-repositories_instructor.ipynb

no changes added to commit (use "git add" and/or "git commit -a")

The last line is the key phrase: “no changes added to commit”. We have changed this file, but we haven’t told Git we will want to save those changes (which we do with git add) nor have we saved them (which we do with git commit). So let’s do that now. It is good practice to always review our changes before saving them. We do this using git diff. This shows us the differences between the current state of the file and the most recently saved version:

git diff

diff --git a/02-git/02-creating-repositories_instructor.ipynb b/02-git/02-creating-repositories_instructor.ipynb
index 0a7156d..4996fde 100644
--- a/02-git/02-creating-repositories_instructor.ipynb
+++ b/02-git/02-creating-repositories_instructor.ipynb
@@ -22,9 +22,32 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/bin/mkdir: cannot create directory ‘planets’: File exists\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "\n"
+     ]
+    }
+   ],
    "source": [
     "cd ~/Desktop\n",
     "mkdir planets\n",
@@ -40,9 +63,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Reinitialized existing Git repository in /home/stuart/Desktop/planets/.git/\n",
+      "\n"
+     ]
+    }
+   ],
    "source": [
     "git init"
    ]
@@ -56,9 +88,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n"
+     ]
+    }
+   ],
    "source": [
     "ls"
    ]
@@ -72,9 +112,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\u001b[0m\u001b[01;34m.\u001b[0m  \u001b[01;34m..\u001b[0m  \u001b[01;34m.git\u001b[0m\n",
+      "\n"
+     ]
+    }
+   ],
    "source": [
     "ls -a"
    ]
@@ -90,9 +139,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "On branch master\n",
+      "\n",
+      "No commits yet\n",
+      "\n",
+      "nothing to commit (create/copy files and use \"git add\" to track)\n",
+      "\n"
+     ]
+    }
+   ],
    "source": [
     "git status"
    ]

The output is cryptic because it is actually a series of commands for tools like editors and patch telling them how to reconstruct one file given the other. If we break it down into pieces:

  1. The first line tells us that Git is producing output similar to the Unix diff command comparing the old and new versions of the file.
  2. The second line tells exactly which versions of the file Git is comparing; df0654a and 315bf3a are unique computer-generated labels for those versions.
  3. The third and fourth lines once again show the name of the file being changed.
  4. The remaining lines are the most interesting, they show us the actual differences and the lines on which they occur. In particular, the + marker in the first column shows where we added a line.

After reviewing our change, it’s time to commit it:

git commit -m "Add concerns about effects of Mars' moons on Wolfman"
git status

On branch master
Your branch is up to date with 'origin/master'.

Changes not staged for commit:
	modified:   02-git/02-creating-repositories_instructor.ipynb

no changes added to commit

On branch master
Your branch is up to date with 'origin/master'.

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

	modified:   02-git/02-creating-repositories_instructor.ipynb

no changes added to commit (use "git add" and/or "git commit -a")

Whoops: Git won’t commit because we didn’t use git add first. Let’s fix that:

git add mars.txt git commit -m “Add concerns about effects of Mars’ moons on Wolfman”

Git insists that we add files to the set we want to commit before actually committing anything. This allows us to commit our changes in stages and capture changes in logical portions rather than only large batches. For example, suppose we’re adding a few citations to relevant research to our thesis. We might want to commit those additions, and the corresponding bibliography entries, but not commit some of our work drafting the conclusion (which we haven’t finished yet).

To allow for this, Git has a special staging area where it keeps track of things that have been added to the current changeset but not yet committed.

# Staging Area

If you think of Git as taking snapshots of changes over the life of a project, git add specifies what will go in a snapshot (putting things in the staging area), and git commit then actually takes the snapshot, and makes a permanent record of it (as a commit). If you don’t have anything staged when you type git commit, Git will prompt you to use git commit -a or git commit --all, which is kind of like gathering everyone for the picture! However, it’s almost always better to explicitly add things to the staging area, because you might commit changes you forgot you made. (Going back to snapshots, you might get the extra with incomplete makeup walking on the stage for the snapshot because you used -a!) Try to stage things manually, or you might find yourself searching for “git undo commit” more than you would like!

Let’s watch as our changes to a file move from our editor to the staging area and into long-term storage. First, we’ll add another line to the file:

nano mars.txt
cat mars.txt





git diff

diff --git a/02-git/02-creating-repositories_instructor.ipynb b/02-git/02-creating-repositories_instructor.ipynb
index 0a7156d..4996fde 100644
--- a/02-git/02-creating-repositories_instructor.ipynb
+++ b/02-git/02-creating-repositories_instructor.ipynb
@@ -22,9 +22,32 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/bin/mkdir: cannot create directory ‘planets’: File exists\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "\n"
+     ]
+    }
+   ],
    "source": [
     "cd ~/Desktop\n",
     "mkdir planets\n",
@@ -40,9 +63,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Reinitialized existing Git repository in /home/stuart/Desktop/planets/.git/\n",
+      "\n"
+     ]
+    }
+   ],
    "source": [
     "git init"
    ]
@@ -56,9 +88,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n"
+     ]
+    }
+   ],
    "source": [
     "ls"
    ]
@@ -72,9 +112,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\u001b[0m\u001b[01;34m.\u001b[0m  \u001b[01;34m..\u001b[0m  \u001b[01;34m.git\u001b[0m\n",
+      "\n"
+     ]
+    }
+   ],
    "source": [
     "ls -a"
    ]
@@ -90,9 +139,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "On branch master\n",
+      "\n",
+      "No commits yet\n",
+      "\n",
+      "nothing to commit (create/copy files and use \"git add\" to track)\n",
+      "\n"
+     ]
+    }
+   ],
    "source": [
     "git status"
    ]

So far, so good: we’ve added one line to the end of the file (shown with a + in the first column). Now let’s put that change in the staging area and see what git diff reports:

git add mars.txt
git diff


diff --git a/02-git/02-creating-repositories_instructor.ipynb b/02-git/02-creating-repositories_instructor.ipynb
index 0a7156d..4996fde 100644
--- a/02-git/02-creating-repositories_instructor.ipynb
+++ b/02-git/02-creating-repositories_instructor.ipynb
@@ -22,9 +22,32 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/bin/mkdir: cannot create directory ‘planets’: File exists\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "\n"
+     ]
+    }
+   ],
    "source": [
     "cd ~/Desktop\n",
     "mkdir planets\n",
@@ -40,9 +63,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Reinitialized existing Git repository in /home/stuart/Desktop/planets/.git/\n",
+      "\n"
+     ]
+    }
+   ],
    "source": [
     "git init"
    ]
@@ -56,9 +88,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n"
+     ]
+    }
+   ],
    "source": [
     "ls"
    ]
@@ -72,9 +112,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\u001b[0m\u001b[01;34m.\u001b[0m  \u001b[01;34m..\u001b[0m  \u001b[01;34m.git\u001b[0m\n",
+      "\n"
+     ]
+    }
+   ],
    "source": [
     "ls -a"
    ]
@@ -90,9 +139,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "On branch master\n",
+      "\n",
+      "No commits yet\n",
+      "\n",
+      "nothing to commit (create/copy files and use \"git add\" to track)\n",
+      "\n"
+     ]
+    }
+   ],
    "source": [
     "git status"
    ]

There is no output: as far as Git can tell, there’s no difference between what it’s been asked to save permanently and what’s currently in the directory. However, if we do this:

git diff --staged

it shows us the difference between the last committed change and what’s in the staging area. Let’s save our changes:

git commit -m "Discuss concerns about Mars' climate for Mummy"

On branch master
Your branch is up to date with 'origin/master'.

Changes not staged for commit:
	modified:   02-git/02-creating-repositories_instructor.ipynb

no changes added to commit

check our status:

git status

On branch master
Your branch is up to date with 'origin/master'.

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

	modified:   02-git/02-creating-repositories_instructor.ipynb

no changes added to commit (use "git add" and/or "git commit -a")

and look at the history of what we’ve done so far:

git log

commit f922c9fa07facba0faa14d2174fcf5c27852eb2a (HEAD -> master, origin/master, origin/HEAD)
Author: Stuart Mumford <stuart@cadair.com>
Date:   Thu Sep 6 18:15:11 2018 +0100

    update notebooks

commit 6053bb89d157b173dda754a895ca3f1076cde97d
Author: Stuart Mumford <stuart@cadair.com>
Date:   Thu Sep 6 12:23:57 2018 +0100

    update notebooks

commit 51172805ab324552bca7a9427eb966a743b4fada
Author: Stuart Mumford <stuart@cadair.com>
Date:   Thu Sep 6 12:03:57 2018 +0100

    update notebooks

commit d26b47bc47fa5768ea2073e3b9683c49a6889908
Author: Stuart Mumford <stuart@cadair.com>
Date:   Thu Sep 6 11:28:09 2018 +0100

    update notebooks

commit 6637293dcb50ae76c9e4a0bf1e2b08dd5a6ce913
Author: Stuart Mumford <stuart@cadair.com>
Date:   Thu Sep 6 11:05:50 2018 +0100

    update notebooks

commit 35247321b5a0ac13471f18bb4703270d94432b73
Author: Stuart Mumford <stuart@cadair.com>
Date:   Wed Sep 5 23:03:45 2018 +0100

    update notebooks

commit 58f1a7f5ee4193bcbf72b15979a8f01a1b99a450
Author: Stuart Mumford <stuart@cadair.com>
Date:   Wed Sep 5 22:28:02 2018 +0100

    update notebooks

commit a967806ebde74eae9d044a895c1651e22e8e0819
Author: Stuart Mumford <stuart@cadair.com>
Date:   Wed Sep 5 16:29:44 2018 +0100

    update notebooks

commit d47a0802cc1913b5073992f9b6fbcc0b72c86307
Author: Stuart Mumford <stuart@cadair.com>
Date:   Wed Sep 5 13:52:51 2018 +0100

    add the csv for timeseries

commit 4135ff84e2b4a552317e7087ae14fdbf0093a2eb
Author: Stuart Mumford <stuart@cadair.com>
Date:   Wed Sep 5 13:51:07 2018 +0100

    update notebooks

commit a9991e8dada1d4de009f1f650a8da84bcfd8757f
Author: Stuart Mumford <stuart@cadair.com>
Date:   Tue Sep 4 11:25:33 2018 +0100

    update notebooks

commit 5bb6f9a228823fb5890d2c0d6b2e9c0b03673668
Author: Stuart Mumford <stuart@cadair.com>
Date:   Tue Sep 4 08:41:44 2018 +0100

    update notebooks

commit dd2848367dff52dd13db252e688a085b0638d2c7
Author: Stuart Mumford <stuart@cadair.com>
Date:   Mon Sep 3 13:24:05 2018 +0100

    update notebooks

commit d3568a1b07b9bf76d89803e610c8ece8d4b94a81
Author: Stuart Mumford <stuart@cadair.com>
Date:   Sun Sep 2 19:25:16 2018 +0100

    update notebooks

commit f5844e2671a8c7a2b212214a4f6c8bd72428f7c3
Author: Stuart Mumford <stuart@cadair.com>
Date:   Sun Sep 2 14:51:57 2018 +0100

    rename to avoid website issues

commit ffe8c9dd48510cd2dcbb964c8ead21b93912be21
Author: Stuart Mumford <stuart@cadair.com>
Date:   Sun Sep 2 14:43:57 2018 +0100

    update notebooks

commit 801632edee8fc310d8500bfaeea8651f099283b3
Author: Stuart Mumford <stuart@cadair.com>
Date:   Sun Sep 2 14:43:13 2018 +0100

    update notebooks

commit 9c74198bf838b7f7127d8fab527e4d96aab72e08
Author: Stuart Mumford <stuart@cadair.com>
Date:   Sun Sep 2 13:46:49 2018 +0100

    Add licence and readme to the lessons repo

commit 08b3d7073b526396de7e31ec6e8bd65d075207b6
Author: Stuart Mumford <stuart@cadair.com>
Date:   Sun Sep 2 12:59:07 2018 +0100

    Add initial dump of rendered lessons

# Word-based diffing

Sometimes, e.g. in the case of the text documents a line-wise diff is too coarse. That is where the --color-words option of git diff comes in very useful as it highlights the changed words using colors.

# Paging the Log

When the output of git log is too long to fit in your screen, git uses a program to split it into pages of the size of your screen. When this “pager” is called, you will notice that the last line in your screen is a :, instead of your usual prompt.

  • To get out of the pager, press Q.
  • To move to the next page, press Spacebar.
  • To search for some_word in all pages, press / and type some_word. Navigate through matches pressing N.

# Limit Log Size

To avoid having git log cover your entire terminal screen, you can limit the number of commits that Git lists by using -N, where N is the number of commits that you want to view. For example, if you only want information from the last commit you can use:

$ git log -1

commit 005937fbe2a98fb83f0ade869025dc2636b4dad5
Author: Vlad Dracula <vlad@tran.sylvan.ia>
Date:   Thu Aug 22 10:14:07 2013 -0400

   Discuss concerns about Mars' climate for Mummy

You can also reduce the quantity of information using the --oneline option:

$ git log --oneline

 * 005937f Discuss concerns about Mars' climate for Mummy
 * 34961b1 Add concerns about effects of Mars' moons on Wolfman
 * f22b25e Start notes on Mars as a base

You can also combine the --oneline options with others. One useful combination is:

$ git log --oneline --graph --all --decorate

* 005937f Discuss concerns about Mars' climate for Mummy (HEAD, master)
* 34961b1 Add concerns about effects of Mars' moons on Wolfman
* f22b25e Start notes on Mars as a base

# Directories

Two important facts you should know about directories in Git.

  1. Git does not track directories on their own, only files within them. Try it for yourself:
$ mkdir directory
$ git status
$ git add directory
$ git status

Note, our newly created empty directory directory does not appear in the list of untracked files even if we explicitly add it (via git add) to our repository. This is the reason why you will sometimes see .gitkeep files in otherwise empty directories. Unlike .gitignore, these files are not special and their sole purpose is to populate a directory so that Git adds it to the repository. In fact, you can name such files anything you like.

  1. If you create a directory in your Git repository and populate it with files, you can add all files in the directory at once by:
git add <directory-with-files>

To recap, when we want to add changes to our repository, we first need to add the changed files to the staging area (git add) and then commit the staged changes to the repository (git commit):

# Choosing a Commit Message

Which of the following commit messages would be most appropriate for the last commit made to mars.txt?

  • “Changes”
  • “Added line ‘But the Mummy will appreciate the lack of humidity’ to mars.txt”
  • “Discuss effects of Mars’ climate on the Mummy”

Solution

Answer 1 is not descriptive enough, and the purpose of the commit is unclear; and answer 2 is redundant to using “git diff” to see what changed in this commit; but answer 3 is good: short, descriptive, and imperative.

# Committing Changes to Git

Which command(s) below would save the changes of myfile.txt to my local Git repository?

$ git commit -m "my recent changes"

$ git init myfile.txt
$ git commit -m "my recent changes"

$ git add myfile.txt
$ git commit -m "my recent changes"

$ git commit -m myfile.txt "my recent changes"

Solution

  • Would only create a commit if files have already been staged.
  • Would try to create a new repository.
  • Is correct: first add the file to the staging area, then commit.
  • Would try to commit a file “my recent changes” with the message myfile.txt.

# Committing Multiple Files

The staging area can hold changes from any number of files that you want to commit as a single snapshot.

  1. Add some text to mars.txt noting your decision to consider Venus as a base
  2. Create a new file venus.txt with your initial thoughts about Venus as a base for you and your friends
  3. Add changes from both files to the staging area, and commit those changes.

Solution

First we make our changes to the mars.txt and venus.txt files:

$ nano mars.txt
$ cat mars.txt

Maybe I should start with a base on Venus.

$ nano venus.txt
$ cat venus.txt

Venus is a nice planet and I definitely should consider it as a base.

Now you can add both files to the staging area. We can do that in one line:

$ git add mars.txt venus.txt

Or with multiple commands:

$ git add mars.txt
$ git add venus.txt

Now the files are ready to commit. You can check that using git status. If you are ready to commit use:

$ git commit -m "Write plans to start a base on Venus"

[master cc127c2]
 Write plans to start a base on Venus
 2 files changed, 2 insertions(+)
 create mode 100644 venus.txt

# `bio` Repository

  • Create a new Git repository on your computer called bio.
  • Write a three-line biography for yourself in a file called me.txt, commit your changes
  • Modify one line, add a fourth line
  • Display the differences between its updated state and its original state.

Solution

If needed, move out of the planets folder:

$ cd ..

Create a new folder called bio and ‘move’ into it:

$ mkdir bio
$ cd bio

Initialise git:

$ git init

Create your biography file me.txt using nano or another text editor. Once in place, add and commit it to the repository:

$ git add me.txt
$ git commit -m'Adding biography file'

Modify the file as described (modify one line, add a fourth line). To display the differences between its updated state and its original state, use git diff:

$ git diff me.txt

# Author and Committer

For each of the commits you have done, Git stored your name twice. You are named as the author and as the committer. You can observe that by telling Git to show you more information about your last commits:

$ git log --format=full

When committing you can name someone else as the author:

$ git commit --author="Vlad Dracula <vlad@tran.sylvan.ia>"

Create a new repository and create two commits: one without the --author option and one by naming a colleague of yours as the author. Run git log and git log --format=full. Think about ways how that can allow you to collaborate with your colleagues.

Solution

$ git add me.txt
$ git commit -m "Update Vlad's bio." --author="Frank N. Stein <franky@monster.com>"

[master 4162a51] Update Vlad's bio.
Author: Frank N. Stein <franky@monster.com>
1 file changed, 2 insertions(+), 2 deletions(-)

$ git log --format=full
commit 4162a51b273ba799a9d395dd70c45d96dba4e2ff
Author: Frank N. Stein <franky@monster.com>
Commit: Vlad Dracula <vlad@tran.sylvan.ia>

Update Vlad's bio.

commit aaa3271e5e26f75f11892718e83a3e2743fab8ea
Author: Vlad Dracula <vlad@tran.sylvan.ia>
Commit: Vlad Dracula <vlad@tran.sylvan.ia>

Vlad's initial bio.

# Key Points

  • git status shows the status of a repository.
  • Files can be stored in a project’s working directory (which users see), the staging area (where the next commit is being built up) and the local repository (where commits are permanently recorded).
  • git add puts files in the staging area.
  • git commit saves the staged content as a new commit in the local repository.
  • Write a commit message that accurately describes your changes.

The material in this notebook is derived from the Software Carpentry lessons © Software Carpentry under the terms of the CC-BY 4.0 license.